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GitLab

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<h3>

Nilesh Patra pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d">12c7a3be</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-08-25T19:58:11+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.1+dfsg</pre>

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</ul>

<h4>24 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a03585ab89eed5e0782a1875b2d8153b97865d30">

<span class="deleted-file">

−

.github/ISSUE_TEMPLATE/bug_report.md

</span>

</a>

</li>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

<span class="deleted-file">

−

.gitignore

</span>

</a>

</li>

<li class="file-stats">

<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">

<span class="deleted-file">

−

.gitmodules

</span>

</a>

</li>

<li class="file-stats">

<a href="#566265babd8b9e3e8d4e94b46a175864edb97dea">

.guix-build

</a>

</li>

<li class="file-stats">

<a href="#05ddeccd55ece967436f502b9e05e738f66ab198">

<span class="new-file">

+

.guix-build-static

</span>

</a>

</li>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

<span class="deleted-file">

−

.travis.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#b8720eeaa38a449b1be8408161b39820b2a11059">

BioD/bio/std/file/fai.d

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<li class="file-stats">

<a href="#5d1df1ee168acbe7e638de550cbfb48ca17d263e">

BioD/bio/std/file/fasta.d

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<li class="file-stats">

<a href="#e3d0b8f292f84509bb59453ca1a4be5cde1977c2">

BioD/bio/std/hts/sam/header.d

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<li class="file-stats">

<a href="#b2270542d41297db1ee0d12698e609ea3ec25ce7">

INSTALL.md

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<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

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<li class="file-stats">

<a href="#544fe3dec8c6dbfa9ec37b21822a8554798b2423">

Makefile.guix

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

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<li class="file-stats">

<a href="#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

RELEASE-NOTES.md

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<li class="file-stats">

<a href="#797aa3f5f6b4cf68af1bed0a90e489e98a0e963d">

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+

TODO.org

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<li class="file-stats">

<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">

VERSION

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<li class="file-stats">

<a href="#7d096d615e9a5f94978a9f4dadcffa52fa06eb23">

doc/design.org

</a>

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<li class="file-stats">

<a href="#d382acb34c28792bbf00055e24fee25e93ea3300">

<span class="deleted-file">

−

man/.gitignore

</span>

</a>

</li>

<li class="file-stats">

<a href="#ac099bc69d055fa991fea205cc9ac0a9aa464fab">

sambamba/flagstat.d

</a>

</li>

<li class="file-stats">

<a href="#3b3ae0b610f6ae26ed107e183c7ee027e957b1ed">

sambamba/main.d

</a>

</li>

<li class="file-stats">

<a href="#b888d326ed4b8a8c518a69a5de5f0ae9bc642ef9">

sambamba/markdup.d

</a>

</li>

<li class="file-stats">

<a href="#b5a32146659405cf1e2a8a45e9e3b9043c26a363">

sambamba/pileup.d

</a>

</li>

<li class="file-stats">

<a href="#a2dfc645061c612393c9e78b784b01f62f7a0e42">

test/benchmark/stats.org

</a>

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<li class="file-stats">

<a href="#3708ce0a178d356e1f2b2d1b351aeb02556a5a7a">

test/test_suite.sh

</a>

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</ul>

<h4>Changes:</h4>

<li id="a03585ab89eed5e0782a1875b2d8153b97865d30">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#a03585ab89eed5e0782a1875b2d8153b97865d30"><strong>.github/ISSUE_TEMPLATE/bug_report.md</strong>

deleted

</a>

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

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bug report 🐞</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="na" style="color: #008080;">about</span><span class="pi">:</span> <span class="s" style="color: #d14;">Create a report to help us improve</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="na" style="color: #008080;">title</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="na" style="color: #008080;">labels</span><span class="pi">:</span> <span class="s" style="color: #d14;">bug</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="na" style="color: #008080;">assignees</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Only bug reports!**</span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">The D version of Sambamba is in maintenance mode. Use the github issue</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">tracker to report bugs <span class="ge" style="font-style: italic;">*only*</span>. For comments, questions and features,</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">please use the google group mailing list as stated on the</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">README</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biod/sambamba/blob/master/README.md</span><span class="p">)</span>!</span>

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

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC15" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Describe the bug**</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">A clear and concise description of what the bug is.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**To Reproduce**</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Steps to reproduce the behavior:</span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p">1.</span> Go to '...'</span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="p">2.</span> Click on '....'</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p">3.</span> Scroll down to '....'</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num 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">

25

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#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="markdown"><span class="p">4.</span> See error</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Expected behavior**</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown">A clear and concise description of what you expected to happen.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Screenshots**</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">If applicable, add screenshots to help explain your problem.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Desktop (please complete the following information):**</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="p">-</span> Browser [e.g. chrome, safari]</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="p">-</span> Version [e.g. 22]</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

33

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Additional context**</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">Add any other context about the problem here.</span>

</pre>

</td>

</tr>

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

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

35

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown">Include a set of BAM/BED files to reproduce the issue</span>

</pre>

</td>

</tr>

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

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37

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</td>

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

<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="p">+</span> bonus points if you try to minimize the test case yourself, as issues are often localized:</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

</td>

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

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="p">  -</span> try to use sambamba slice to first extract the reference where the error occurs</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="p">  -</span> if that succeeds (the error is still reproducible), continue to crop the file in binary-search fashion</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong>

deleted

</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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1

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.dub/</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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

</td>

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

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">dub.selections.json</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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</td>

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

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">lz4/</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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

</td>

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

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

</pre>

</td>

</tr>

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

5

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">test.log</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">/*.bai</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC12" class="line" lang="plaintext">/*.crai</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">!meson_options.txt</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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17

</td>

<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC17" class="line" lang="plaintext">*.out</span>

</pre>

</td>

</tr>

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18

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">/utils/ldc_version_info_.d</span>

</pre>

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19

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">profile.data</span>

</pre>

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20

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">profile.raw</span>

</pre>

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21

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">output</span>

</pre>

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22

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">builddir</span></pre>

</td>

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</table>

<br>

</li>

<li id="7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44"><strong>.gitmodules</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">[submodule "lz4"]</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">      path = lz4</span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">      url = https://github.com/lz4/lz4.git</span></pre>

</td>

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</table>

<br>

</li>

<li id="566265babd8b9e3e8d4e94b46a175864edb97dea">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#566265babd8b9e3e8d4e94b46a175864edb97dea"><strong>.guix-build</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># This command creates a build container for Sambamba using GNU Guix</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"></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib</span></pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics \</span>

</pre>

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib $*</span></pre>

</td>

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</table>

<br>

</li>

<li id="05ddeccd55ece967436f502b9e05e738f66ab198">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#05ddeccd55ece967436f502b9e05e738f66ab198"><strong>.guix-build-static</strong></a>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># This command creates a build container for Sambamba using GNU Guix</span>

</pre>

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2

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

</pre>

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3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib:static</span></pre>

</td>

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<br>

</li>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>

deleted

</a>

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1

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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="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">d</span></span>

</pre>

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2

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

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">ldc</span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># ARM64 testing is under development</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">  <span class="na" style="color: #008080;">allow_failures</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml">  <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

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11

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">arm64</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make check</span></span></pre>

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<br>

</li>

<li id="b8720eeaa38a449b1be8408161b39820b2a11059">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#b8720eeaa38a449b1be8408161b39820b2a11059"><strong>BioD/bio/std/file/fai.d</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="41" style="width: 35px; color: rgba(0,0,0,0.3); 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="41" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -41,12 +41,6 @@ struct FaiRecord {</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="d">    <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="d">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"%s\t%s\t%s\t%s\t%s"</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">seqLen</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">lineLen</span><span class="p">,</span> <span class="n" style="color: #333;">lineOffset</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="d">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="d">    <span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rec</span> <span class="p">=</span> <span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="d">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="d">        <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="s" style="color: #d14;">"\r\n"</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="d">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t52"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="d">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="d">    <span class="k" style="font-weight: 600;">this</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">str</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">res</span> <span class="p">=</span> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); 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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,10 +50,6 @@ struct FaiRecord {</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="d">        <span class="n" style="color: #333;">lineLen</span> <span class="p">=</span> <span class="n" style="color: #333;">to</span><span class="p">!</span><span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="d">        <span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="p">(</span><span class="n" style="color: #333;">to</span><span class="p">!</span><span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])-</span><span class="n" style="color: #333;">lineLen</span><span class="p">)</span> <span class="p">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">?</span> <span class="s" style="color: #d14;">"\n"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"\r\n"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="d">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="d">    <span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="p">=</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="d">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="d">    <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="d">    <span class="k" style="font-weight: 600;">this</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">lineTerm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">seqLen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">lineLen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">offset</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="d">        <span class="k" style="font-weight: 600;">this</span><span class="p">.</span><span class="n" style="color: #333;">header</span> <span class="p">=</span> <span class="n" style="color: #333;">header</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,48 +58,25 @@ struct FaiRecord {</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="d">        <span class="k" style="font-weight: 600;">this</span><span class="p">.</span><span class="n" style="color: #333;">lineLen</span> <span class="p">=</span> <span class="n" style="color: #333;">lineLen</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="d">        <span class="k" style="font-weight: 600;">this</span><span class="p">.</span><span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="n" style="color: #333;">lineTerm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="d">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="d">    <span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="d">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">).</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="d"><span class="p">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="d"></span>

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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">readFai</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="d">    <span class="n" style="color: #333;"><span class="idiff left right">File</span></span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">readFai</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;"><span class="idiff left right">fai_</span>filename</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="d">    <span class="k" style="font-weight: 600;"><span class="idiff left">auto</span></span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">fai_</span>filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">byLineCopy</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="d">            <span class="p">.</span><span class="n" style="color: #333;">map</span><span class="p">!(</span><span class="n" style="color: #333;">x</span> <span class="p">=></span> <span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">));</span></span>

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67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

81

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">faiString</span> <span class="p">=</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testIndex</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test1.fa.fai"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// scope(exit) remove(testIndex);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

85

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

86

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="n" style="color: #333;">faiString</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

87

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

88

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">recs</span> <span class="p">=</span> <span class="n" style="color: #333;">readFai</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">).</span><span class="n" style="color: #333;">array</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// assert(recs.length == 1);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">is</span><span class="p">(</span><span class="k" style="font-weight: 600;">typeof</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])==</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="n" style="color: #333;">faiString</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC92" class="line" lang="d"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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

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

</pre>

</td>

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<td class="old_line diff-line-num" 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">

94

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<td class="new_line diff-line-num" 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">

69

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

<pre style="margin: 0;"> <span id="LC69" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">makeIndex</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">records</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<td class="new_line diff-line-num" 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

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

<pre style="margin: 0;"> <span id="LC70" class="line" lang="d">    <span class="n" style="color: #333;">FaiRecord</span><span class="p">[</span><span class="nb" style="color: #0086b3;">string</span><span class="p">]</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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<td class="new_line diff-line-num" 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

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

<pre style="margin: 0;"> <span id="LC71" class="line" lang="d">    <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">;</span> <span class="n" style="color: #333;">records</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

97

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<td class="new_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC97" class="line" lang="d">      <span class="idiff left right">  </span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">record</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="d">      <span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">record</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

98

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

73

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

</td>

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

74

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

<pre style="margin: 0;"> <span id="LC74" class="line" lang="d">    <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">rehash</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

</td>

<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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

<pre style="margin: 0;"> <span id="LC76" class="line" lang="d"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC102" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

103

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC103" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">records</span> <span class="p">=</span> <span class="n" style="color: #333;">to</span><span class="p">!(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">[])([</span><span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

104

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC104" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">i</span> <span class="p">=</span> <span class="n" style="color: #333;">makeIndex</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC105" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">length</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="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC106" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="s" style="color: #d14;">"chr2"</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC107" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">]</span> <span class="p">==</span>  <span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">));</span></span>

</pre>

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

<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

108

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC108" class="line" lang="d"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

109

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC109" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC110" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">buildFai</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

</td>

<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

</td>

<td class="new_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC112" class="line" lang="d">    <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

<pre style="margin: 0;">+<span id="LC78" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">buildFai</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">fasta_filename</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC79" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">fasta_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="d">    <span class="n" style="color: #333;">FaiRecord</span><span class="p">[]</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="d">    <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">byLine</span><span class="p">(</span><span class="n" style="color: #333;">KeepTerminator</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="p">).</span><span class="n" style="color: #333;">take</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">front</span><span class="p">.</span><span class="n" style="color: #333;">endsWith</span><span class="p">(</span><span class="s" style="color: #d14;">"\r\n"</span><span class="p">)</span> <span class="p">?</span> <span class="s" style="color: #d14;">"\r\n"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">seek</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 unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -133,10 +100,11 @@ auto buildFai(string filename) {</td>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="d"></span>

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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" 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="d"></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="d"><span class="k" style="font-weight: 600;">version</span><span class="p">(</span><span class="n" style="color: #333;">Broken</span><span class="p">)</span> <span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC105" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testFa</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test1.fa"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// scope(exit) remove(testFa);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fa</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fa</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC108" class="line" lang="d">    <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">q"(</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="d"><span class="s" style="color: #d14;">        >chr1</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgc</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,6 +112,7 @@ unittest {</td>

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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

144

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgcacgtgagtgcacgtgagtgc</span></span>

</pre>

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113

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgcacgtgagtgc</span></span>

</pre>

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146

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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="d"><span class="s" style="color: #d14;">    )"</span><span class="p">.</span><span class="n" style="color: #333;">outdent</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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="d">    <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

147

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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="d">    <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">recs</span> <span class="p">=</span> <span class="n" style="color: #333;">buildFai</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">).</span><span class="n" style="color: #333;">array</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">==</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">toString</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -151,3 +120,40 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr1\t10\t6\t10\t11"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t50\t23\t30\t31"</span><span class="p">);</span></span>

</pre>

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

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="d"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">records</span> <span class="p">=</span> <span class="n" style="color: #333;">to</span><span class="p">!(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">[])([</span><span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">i</span> <span class="p">=</span> <span class="n" style="color: #333;">makeIndex</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">length</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="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="s" style="color: #d14;">"chr2"</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">]</span> <span class="p">==</span>  <span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"><span class="k" style="font-weight: 600;">version</span><span class="p">(</span><span class="n" style="color: #333;">Broken</span><span class="p">)</span> <span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">faiString</span> <span class="p">=</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testIndex</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test1.fa.fai"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC136" class="line" lang="d">  <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="n" style="color: #333;">faiString</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC137" class="line" lang="d">  <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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

<pre style="margin: 0;">+<span id="LC139" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">recs</span> <span class="p">=</span> <span class="n" style="color: #333;">readFai</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">).</span><span class="n" style="color: #333;">array</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC140" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">length</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="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC141" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">is</span><span class="p">(</span><span class="k" style="font-weight: 600;">typeof</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])==</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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

<pre style="margin: 0;">+<span id="LC142" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="n" style="color: #333;">faiString</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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

<pre style="margin: 0;">+<span id="LC143" class="line" lang="d"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rec</span> <span class="p">=</span> <span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="d">  <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="s" style="color: #d14;">"\r\n"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t52"</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="d"></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="p">=</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="d"><span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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

</pre>

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<td class="new_line diff-line-num new" 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="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">FaiRecord</span><span class="p">(</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">).</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2\t10\t4\t50\t51"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="d"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="5d1df1ee168acbe7e638de550cbfb48ca17d263e">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#5d1df1ee168acbe7e638de550cbfb48ca17d263e"><strong>BioD/bio/std/file/fasta.d</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,7 +157,7 @@ struct Region {</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fastaRecords</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC159" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="d">    <span class="n" style="color: #333;"><span class="idiff left">File</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="d">    <span class="k" style="font-weight: 600;"><span class="idiff left">auto</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="p"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="d">    <span class="n" style="color: #333;">FastaRecord</span><span class="p">[]</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="d">    <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">lineTerm</span> <span class="p">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">byLine</span><span class="p">(</span><span class="n" style="color: #333;">KeepTerminator</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="p">).</span><span class="n" style="color: #333;">take</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">front</span><span class="p">.</span><span class="n" style="color: #333;">endsWith</span><span class="p">(</span><span class="s" style="color: #d14;">"\r\n"</span><span class="p">)</span> <span class="p">?</span> <span class="s" style="color: #d14;">"\r\n"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -180,7 +180,7 @@ auto fastaRecords(string filename) {</td>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="d"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="d"></span>

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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="d"><span class="k" style="font-weight: 600;"><span class="idiff left">version</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Broken</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC184" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testFa</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test2.fa"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// scope(exit) testFa.remove;</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="d"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); 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="194" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -194,6 +194,7 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="d"><span class="s" style="color: #d14;">        >chr3 hrsv | Kilifi | partial sequence</span></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="d"><span class="s" style="color: #d14;">        CATGTTATTACAAGTAGTGATATTTGCCCTAATAATAATATTGTAGTGAAATCCAATTTCACAACAATGC</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="d"><span class="s" style="color: #d14;">    )"</span><span class="p">.</span><span class="n" style="color: #333;">outdent</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="d">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">records</span> <span class="p">=</span> <span class="n" style="color: #333;">fastaRecords</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">records</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">==</span> <span class="mi" style="color: #099;">3</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); 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="220" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -219,7 +220,7 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC221" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC222" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fastaRegions</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">string</span><span class="p">[]</span> <span class="n" style="color: #333;">queries</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="d">    <span class="n" style="color: #333;"><span class="idiff left">File</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="d">    <span class="k" style="font-weight: 600;"><span class="idiff left">auto</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="p"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC224" class="line" lang="d">    <span class="n" style="color: #333;">FaiRecord</span><span class="p">[</span><span class="nb" style="color: #0086b3;">string</span><span class="p">]</span> <span class="n" style="color: #333;">index</span> <span class="p">=</span> <span class="n" style="color: #333;">makeIndex</span><span class="p">(</span><span class="n" style="color: #333;">readFai</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">~=</span><span class="s" style="color: #d14;">".fai"</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="d">    <span class="n" style="color: #333;">Region</span><span class="p">[]</span> <span class="n" style="color: #333;">regions</span> <span class="p">=</span> <span class="n" style="color: #333;">to</span><span class="p">!(</span><span class="n" style="color: #333;">Region</span><span class="p">[])(</span><span class="n" style="color: #333;">queries</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC226" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">res</span> <span class="p">=</span> <span class="n" style="color: #333;">fetchFastaRegions</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); 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="228" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -227,7 +228,7 @@ auto fastaRegions(string filename, string[] queries) {</td>

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<td class="new_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC228" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC230" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fetchFastaRegions</span><span class="p">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">FaiRecord</span><span class="p">[</span><span class="nb" style="color: #0086b3;">string</span><span class="p">]</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">Region</span><span class="p">[]</span> <span class="n" style="color: #333;">regions</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="d"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fetchFastaRegions</span><span class="p">(</span><span class="n" style="color: #333;">File</span> <span class="p"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">FaiRecord</span><span class="p">[</span><span class="nb" style="color: #0086b3;">string</span><span class="p">]</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">Region</span><span class="p">[]</span> <span class="n" style="color: #333;">regions</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC232" class="line" lang="d"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="d">    <span class="n" style="color: #333;">FastaRecord</span><span class="p">[]</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="d"></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">@@ -251,10 +252,10 @@ auto fetchFastaRegions(File fasta, FaiRecord[string] index, Region[] regions) {</td>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="d"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="d"></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="d"><span class="k" style="font-weight: 600;"><span class="idiff left">version</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Broken</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testFa</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test3.fa"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="d">  <span class="c1" style="color: #998; font-style: italic;">// scope(exit) remove(testFa);</span></span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fa</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fa</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="d">  <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">q"(</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="d"><span class="s" style="color: #d14;">        >chr1</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgc</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -262,6 +263,7 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgcacgtgagtgcacgtgagtgc</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="d"><span class="s" style="color: #d14;">        acgtgagtgcacgtgagtgc</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="d"><span class="s" style="color: #d14;">    )"</span><span class="p">.</span><span class="n" style="color: #333;">outdent</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="d">  <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="d">  <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">faiString</span> <span class="p">=</span> <span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="d"><span class="s" style="color: #d14;">        chr1\t10\t6\t10\t11</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -269,18 +271,19 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="d"><span class="s" style="color: #d14;">    "</span><span class="p">.</span><span class="n" style="color: #333;">outdent</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">();</span></span>

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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC272" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">testIndex</span> <span class="p">=</span> <span class="n" style="color: #333;">tempDir</span><span class="p">.</span><span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="s" style="color: #d14;">"test3.fa.fai"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="d">  <span class="c1" style="color: #998; font-style: italic;">// scope(exit) testIndex.remove;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f2</span> <span class="p">=</span> <span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="d">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">f2</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">testIndex</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="d">  <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="n" style="color: #333;">faiString</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="d">  <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC277" class="line" lang="d">  <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC279" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">regions</span> <span class="p">=</span> <span class="n" style="color: #333;">fastaRegions</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"chr1:4-6"</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr2:36-45"</span><span class="p">]);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC281" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">header</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr1:4-6"</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">3</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">3</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">regions</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff right">()</span></span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sequence</span> <span class="p">==</span> <span class="s" style="color: #d14;">"tga"</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">lineLen</span> <span class="p">==</span> <span class="mi" style="color: #099;">10</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">header</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2:36-45"</span> <span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">10</span> <span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">10</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">regions</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff right">()</span></span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sequence</span> <span class="p">==</span> <span class="s" style="color: #d14;">"agtgcacgtg"</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">lineLen</span> <span class="p">==</span> <span class="mi" style="color: #099;">30</span> <span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); 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="297" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -294,7 +297,7 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="d">    <span class="n" style="color: #333;">regions</span> <span class="p">=</span> <span class="n" style="color: #333;">fastaRegions</span><span class="p">(</span><span class="n" style="color: #333;">testFa</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"chr2"</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span><span class="n" style="color: #333;">length</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="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC299" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">header</span> <span class="p">==</span> <span class="s" style="color: #d14;">"chr2"</span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">50</span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="p">==</span> <span class="mi" style="color: #099;">50</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">regions</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff right">()</span></span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sequence</span> <span class="p">==</span> <span class="s" style="color: #d14;">"acgtgagtgcacgtgagtgcacgtgagtgcacgtgagtgcacgtgagtgc"</span> <span class="p">);</span></span>

</pre>

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299

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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span> <span class="n" style="color: #333;">regions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">lineLen</span> <span class="p">==</span> <span class="mi" style="color: #099;">30</span> <span class="p">);</span></span>

</pre>

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300

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<td class="new_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

303

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="d"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="e3d0b8f292f84509bb59453ca1a4be5cde1977c2">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#e3d0b8f292f84509bb59453ca1a4be5cde1977c2"><strong>BioD/bio/std/hts/sam/header.d</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="215" style="width: 35px; color: rgba(0,0,0,0.3); 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="215" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -215,12 +215,16 @@ private {</td>

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215

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

215

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

<pre style="margin: 0;"> <span id="LC215" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

216

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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

216

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="d"><span class="k" style="font-weight: 600;">mixin</span> <span class="n" style="color: #333;">HeaderLineStruct</span><span class="p">!(</span><span class="s" style="color: #d14;">"HdLine"</span><span class="p">,</span> <span class="s" style="color: #d14;">"@HD"</span><span class="p">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

217

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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

217

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"format_version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"VN"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

218

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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC218" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"sorting_order"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SO"</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

218

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"grouping"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GO"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

219

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

<pre style="margin: 0;">+<span id="LC219" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"sorting_order"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SO"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

220

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"sub_sorting_order"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SS"</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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<td class="new_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

221

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

<pre style="margin: 0;"> <span id="LC221" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

220

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<td class="new_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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

<pre style="margin: 0;"> <span id="LC222" class="line" lang="d"><span class="k" style="font-weight: 600;">mixin</span> <span class="n" style="color: #333;">HeaderLineStruct</span><span class="p">!(</span><span class="s" style="color: #d14;">"SqLine"</span><span class="p">,</span> <span class="s" style="color: #d14;">"@SQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

221

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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SN"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

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

<pre style="margin: 0;"> <span id="LC224" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"LN"</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

225

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"alternative_names"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AN"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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<td class="new_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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

<pre style="margin: 0;"> <span id="LC226" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"assembly"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AS"</span><span class="p">),</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

227

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"description"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DS"</span><span class="p">),</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

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<td class="new_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC228" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"md5"</span><span class="p">,</span> <span class="s" style="color: #d14;">"M5"</span><span class="p">),</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"species"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SP"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC230" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"uri"</span><span class="p">,</span> <span class="s" style="color: #d14;">"UR"</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); 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="232" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -228,6 +232,7 @@ mixin HeaderLineStruct!("SqLine", "@SQ", "name",</td>

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228

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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

232

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="d"><span class="k" style="font-weight: 600;">mixin</span> <span class="n" style="color: #333;">HeaderLineStruct</span><span class="p">!(</span><span class="s" style="color: #d14;">"RgLine"</span><span class="p">,</span> <span class="s" style="color: #d14;">"@RG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"identifier"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"identifier"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"barcode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BC"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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<td class="new_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC236" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"sequencing_center"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CN"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

232

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<td class="new_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

237

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"description"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DS"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

238

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="d">          <span class="n" style="color: #333;">Field</span><span class="p">!(</span><span class="s" style="color: #d14;">"date"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DT"</span><span class="p">),</span></span>

</pre>

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<br>

</li>

<li id="b2270542d41297db1ee0d12698e609ea3ec25ce7">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#b2270542d41297db1ee0d12698e609ea3ec25ce7"><strong>INSTALL.md</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ and run our development setup (gold was added lately by ldc)</td>

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

18

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

18

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

</pre>

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

19

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

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make clean</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="new_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC21" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -f Makefile.guix -j 4</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right">env CC=gcc </span>make -f Makefile.guix -j 4</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -f Makefile.guix check</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">this way all dependencies are isolated. To create a static release use</span>

</pre>

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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">@@ -31,7 +31,30 @@ We use GNU Guix containers for development. Install Guix and run a build</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">container with</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="sb" style="color: #d14;">    . .guix-build</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -f Makefile.guix</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -f Makefile.guix clean</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;">    # build the debug version</span></span>

</pre>

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

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;">    env CC=gcc make -f Makefile.guix lz4-static -j 8</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;">    env CC=gcc make -f Makefile.guix -j 8</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -f Makefile.guix check</span></span>

</pre>

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

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); 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="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">Note that this also works in the emacs shell.</span></pre>

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

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">To make the static release:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown"><span class="sb" style="color: #d14;">    env CC=gcc make -f Makefile.guix static</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown">It gives some errors, but should work:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown"><span class="sb" style="color: #d14;">    ./bin/sambamba</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" 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="markdown">When you only get unit tests disable them with <span class="sb" style="color: #d14;">`--DRT-testmode=run-main`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" 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="markdown">Note that this all also works in the emacs shell.</span>

</pre>

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

</pre>

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<td class="new_line diff-line-num new" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Guix VM</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix package -i qemu -p ~/opt/qemu</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;">    . ~/opt/qemu/etc/profile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">Download the bootable image from https://guix.gnu.org/en/download/ and</span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">start it with, for example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="sb" style="color: #d14;">    qemu-system-x86_64    -nic user,model=virtio-net-pci    -enable-kvm -m 1024    -device virtio-blk,drive=myhd    -drive if=none,file=guix-system-vm-image-1.2.0.x86_64-linux,id=myhd</span></span></pre>

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<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,14 +52,14 @@ coverage:                          DFLAGS += -cov</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"><span class="nl">release static pgo-static</span><span class="o" style="font-weight: 600;">:</span>         <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -O3 -release -enable-inlining -boundscheck=off -L-lz</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="make"><span class="nl">static</span><span class="o" style="font-weight: 600;">:</span>                            <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -static -L-Bstatic</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="make"><span class="nl">static</span><span class="o" style="font-weight: 600;">:</span>                            <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -static -L-Bstatic<span class="idiff left right"> -link-defaultlib-shared=false</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC57" class="line" lang="make"><span class="nl">pgo-static</span><span class="o" style="font-weight: 600;">:</span>                        <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -fprofile-instr-use=profile.data</span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" 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">

59

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<td class="new_line diff-line-num" 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="make"><span class="nl">lz4-static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lz4/lib/liblz4.a</span></span>

</pre>

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC61" class="line" lang="make"><span class="nl">lz4/lib/liblz4.a</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

62

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<td class="new_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="make">  <span class="nb" style="color: #0086b3;">cd </span>lz4/lib <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left right">gcc</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-c</span> lz4.c lz4hc.c lz4frame.c xxhash.c <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(AR)</span> rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" 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="make">  <span class="nb" style="color: #0086b3;">cd </span>lz4/lib <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$(CC)</span></span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-c</span> lz4.c lz4hc.c lz4frame.c xxhash.c <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(AR)</span> rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"><span class="nl">utils/ldc_version_info_.d</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make">  python3 ./gen_ldc_version_info.py <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> which ldmd2<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> utils/ldc_version_info_.d</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="544fe3dec8c6dbfa9ec37b21822a8554798b2423">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#544fe3dec8c6dbfa9ec37b21822a8554798b2423"><strong>Makefile.guix</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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ LIBS   = -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a</td>

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

31

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

31

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

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

</pre>

</td>

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

32

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<td class="new_line diff-line-num" 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="LC32" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS_STATIC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(DLIBS)</span> lz4/lib/liblz4.a</span>

</pre>

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

33

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

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

<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">SRC</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> main.d utils/<span class="k" style="font-weight: 600;">*</span>.d thirdparty/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> BioD/contrib/undead/<span class="k" style="font-weight: 600;">*</span>.d BioD/contrib/undead/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> sambamba/<span class="k" style="font-weight: 600;">*</span>.d sambamba/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d sambamba/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(SRC:.d=.o)</span><span class="idiff left right"> utils/ldc_version_info_.o</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="make"><span class="nv" style="color: #008080;">OBJ</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(SRC:.d=.o)</span></span>

</pre>

</td>

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

35

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

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

<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nv" style="color: #008080;">OUT</span>    <span class="o" style="font-weight: 600;">=</span> bin/sambamba-<span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">cat </span>VERSION<span class="nf" style="color: #900; font-weight: 600;">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nl">static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">OUT += -static</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,7 +72,7 @@ utils/ldc_version_info_.d:</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="LC72" class="line" lang="make"><span class="nl">ldc_version_info</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">utils/ldc_version_info_.d</span></span>

</pre>

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

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

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

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="make"><span class="nl">lz4/lib/liblz4.a</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="make">  <span class="nb" style="color: #0086b3;">cd </span>lz4/lib <span class="o" style="font-weight: 600;">&&</span> <span class="idiff left right">gcc</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-c</span> lz4.c lz4hc.c lz4frame.c xxhash.c <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(AR)</span> rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o</span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="make">  <span class="nb" style="color: #0086b3;">cd </span>lz4/lib <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$(CC)</span></span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-c</span> lz4.c lz4hc.c lz4frame.c xxhash.c <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(AR)</span> rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC76" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC77" class="line" lang="make"><span class="nl">lz4-static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">lz4/lib/liblz4.a</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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="make"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,7 +116,7 @@ clean-c:</td>

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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-v</span> lz4/lib/<span class="k" style="font-weight: 600;">*</span>.[oa]</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC117" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC118" class="line" lang="make"><span class="nl">clean-d</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$(OBJ)</span> <span class="nv" style="color: #008080;">$(OUT)</span> trace.<span class="o" style="font-weight: 600;">{</span>def,log<span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$(OBJ)</span> <span class="nv" style="color: #008080;">$(OUT)</span> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>trace.{def,log</span><span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC120" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-v</span> bin/<span class="k" style="font-weight: 600;">*</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="make"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="make"><span class="nl">clean-tests</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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1

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/biod/sambamba.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/biod/sambamba) <span class="p">[</span><span class="nv" style="color: #008080;">![AnacondaBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/sambamba) <span class="p">[</span><span class="nv" style="color: #008080;">![DL</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/sambamba/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/sambamba) <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![AnacondaVersion</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/sambamba/badges/version.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">] </span><span class="p">[</span><span class="nv" style="color: #008080;">![BrewBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg</span><span class="p">)</span>](https://github.com/brewsci/homebrew-bio) <span class="p">[</span><span class="nv" style="color: #008080;">![GuixBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/gnuguix-sambamba-brightgreen.svg</span><span class="p">)</span>](https://www.gnu.org/software/guix/packages/S/) <span class="p">[</span><span class="nv" style="color: #008080;">![DebianBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badges.debian.net/badges/debian/testing/sambamba/version.svg</span><span class="p">)</span>](https://packages.debian.org/testing/sambamba)</span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/biod/sambamba.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/biod/sambamba) <span class="p">[</span><span class="nv" style="color: #008080;">![AnacondaBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/sambamba) <span class="p">[</span><span class="nv" style="color: #008080;">![DL</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/sambamba/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/sambamba) <span class="p">[</span><span class="nv" style="color: #008080;">![BrewBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg</span><span class="p">)</span>](https://github.com/brewsci/homebrew-bio) <span class="p">[</span><span class="nv" style="color: #008080;">![GuixBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/gnuguix-sambamba-brightgreen.svg</span><span class="p">)</span>](https://www.gnu.org/software/guix/packages/S/) <span class="p">[</span><span class="nv" style="color: #008080;">![DebianBadge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badges.debian.net/badges/debian/testing/sambamba/version.svg</span><span class="p">)</span>](https://packages.debian.org/testing/sambamba)</span>

</pre>

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2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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

</pre>

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3

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># SAMBAMBA</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c"><strong>RELEASE-NOTES.md</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="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.8.1 (20210731)</span></span>

</pre>

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<td class="old_line diff-line-num" 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

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2

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.8.0 (2020??)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Some FASTA unittests break when they write to disk and read after -</span>

</pre>

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">  marked with ~version(Broken)~</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Fix build for LDC 1.26.0 and LLVM 9.0.1 - some speed improvement</span>

</pre>

</td>

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<td class="new_line diff-line-num new" 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="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.8.0 (20201130)</span></span>

</pre>

</td>

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

3

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

8

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">Maintainance release and bug fixes: this is a special release where we</span>

</pre>

</td>

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

5

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">removed all CRAM support. The added value of CRAM in sambamba was</span>

</pre>

</td>

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

6

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">limited because it was using essentially the same htslib backend as</span>

</pre>

</td>

</tr>

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

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

7

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">samtools. Removing the htslib dependency removes one maintenance</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">headache. See also https://github.com/biod/sambamba/issues/425</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<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="markdown">headache. See also https://github.com/biod/sambamba/issues/425.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<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="markdown"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

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<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="markdown">BioD was also moved back into the main trunk. We separated it in the</span>

</pre>

</td>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

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<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="markdown">past, but as there is no development there we might as well have it in</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

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<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="markdown">Sambamba (again).</span>

</pre>

</td>

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

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

9

</td>

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

18

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

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

19

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">+</span> Removed CRAM support and htslib dependency with ec78eabfbdebd620cf5d4a4d8232692184eacbf7</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Removed BioD source tree back into Sambamba</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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

<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">+</span> Sambamba builds on ARM64 (see <span class="p">[</span><span class="nv" style="color: #008080;">Travis-CI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/github/biod/sambamba</span><span class="p">)</span>)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

<td class="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">+</span> Changed github issue tracker template to report bugs only</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p">+</span> Removed BioD source tree back into Sambamba</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Added FASTA handlers, indexing and slicing (thanks @NickRoz1)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Updated slice.d (thanks @NickRoz1)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Fixed FASTA file handlers not closing cdc5f84c5b6135eedeaf5cba265e3eb9a3c23227</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Added badges to the top of README</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="markdown"><span class="p">+</span> Added Meson build system for Debian (thanks Matthias @ximion)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">+</span> Fixed Python2 -> Python3 stuff (thanks Matthias @ximion)</span>

</pre>

</td>

</tr>

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

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

14

</td>

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

29

</td>

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

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

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.7.1 (20191128)</span></span>

</pre>

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

</pre>

</td>

</tr>

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<br>

</li>

<li id="797aa3f5f6b4cf68af1bed0a90e489e98a0e963d">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#797aa3f5f6b4cf68af1bed0a90e489e98a0e963d"><strong>TODO.org</strong></a>

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1

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

</pre>

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

</pre>

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3

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

</pre>

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

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">+ Make markdup single pass for pipes, see #421</span></pre>

</td>

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<br>

</li>

<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.8.<span class="idiff left right">0</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.8.<span class="idiff left right">1</span></span></pre>

</td>

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<br>

</li>

<li id="7d096d615e9a5f94978a9f4dadcffa52fa06eb23">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#7d096d615e9a5f94978a9f4dadcffa52fa06eb23"><strong>doc/design.org</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>

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3

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

</pre>

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4

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

</pre>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Because of its great multi-core performance Sambamba has served over</span>

</pre>

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6

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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">five</span> years in sequencing centers [[https://groups.google.com/d/msg/sambamba-discussion/fIgrrUa441o/XG7Rt3dFAQAJ][around the world]]. Here we start on a</span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="plaintext"><span class="idiff left right">eight</span> years in sequencing centers [[https://groups.google.com/d/msg/sambamba-discussion/fIgrrUa441o/XG7Rt3dFAQAJ][around the world]]. Here we start on a</span>

</pre>

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

7

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">new design (sambamba2) that should improve performance and, perhaps</span>

</pre>

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">more importantly, make the building blocks more composable. D has</span>

</pre>

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">proven to be a great language for multi-core performance and code</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); 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="80" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -80,3 +80,6 @@ and should be capable of writing to a log file.</td>

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80

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">The original markdup routine is written in sambamba/markdup.d. It</span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">maintains state in a structure called IndexedBamRead with an index</span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">value and the read object.</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>

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<td class="new_line diff-line-num new" 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="plaintext">Note that Markdup does two reader passes. This prevents piping</span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">through stdin. A future version may do a single pass.</span></pre>

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<br>

</li>

<li id="d382acb34c28792bbf00055e24fee25e93ea3300">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#d382acb34c28792bbf00055e24fee25e93ea3300"><strong>man/.gitignore</strong>

deleted

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1

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*.html</span></pre>

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<li id="ac099bc69d055fa991fea205cc9ac0a9aa464fab">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#ac099bc69d055fa991fea205cc9ac0a9aa464fab"><strong>sambamba/flagstat.d</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); 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="56" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -56,8 +56,11 @@ void computeFlagStatistics(R)(R alignments) {</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="d">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="d"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="d"></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">param</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="d">    <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s + %s %s"</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">description</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tabular</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="d">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tabular</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="d">        <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s,%s,%s"</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">param</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="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="d">        <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s + %s %s"</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">description</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="d"><span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">percent</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">to</span><span class="p">!</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="p">/</span> <span class="n" style="color: #333;">b</span> <span class="p">*</span> <span class="mf" style="color: #099;">100.0</span><span class="p">;</span> <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</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">@@ -67,8 +70,11 @@ string percentStr(ulong a, ulong b) {</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"%.2f%%"</span><span class="p">,</span> <span class="n" style="color: #333;">percent</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="d"><span class="p">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">total</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="d">    <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s + %s %s (%s:%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">description</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">ulong</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">total</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tabular</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" 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="d">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tabular</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="d">        <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s,%s:%s,%s:%s"</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">percentStr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">total</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">percentStr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">total</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]));</span></span>

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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="d">    <span class="k" style="font-weight: 600;">else</span></span>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="d">        <span class="n" style="color: #333;">writefln</span><span class="p">(</span><span class="s" style="color: #d14;">"%s + %s %s (%s:%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">description</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="d">             <span class="n" style="color: #333;">percentStr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">total</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="d">             <span class="n" style="color: #333;">percentStr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">total</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]));</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -86,17 +92,21 @@ void printUsage() {</td>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"            use NTHREADS for decompression"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"         -p, --show-progress"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"            show progressbar in STDERR"</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"         -b, --tabular"</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"            output in csv format"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="d"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" 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="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flagstat_main</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span><span class="p">[]</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC100" class="line" lang="d">    <span class="nb" style="color: #0086b3;">size_t</span> <span class="n" style="color: #333;">threads</span> <span class="p">=</span> <span class="n" style="color: #333;">totalCPUs</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC101" class="line" lang="d">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">show_progress</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="d">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tabular</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC104" class="line" lang="d">    <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC105" class="line" lang="d">        <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC106" class="line" lang="d">               <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">getopt</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">caseSensitive</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="d">               <span class="s" style="color: #d14;">"nthreads|t"</span><span class="p">,</span>      <span class="p">&</span><span class="n" style="color: #333;">threads</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="d">               <span class="s" style="color: #d14;">"show-progress|p"</span><span class="p">,</span> <span class="p">&</span><span class="n" style="color: #333;">show_progress</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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="d">               <span class="s" style="color: #d14;">"show-progress|p"</span><span class="p">,</span> <span class="p">&</span><span class="n" style="color: #333;">show_progress</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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="d">               <span class="s" style="color: #d14;">"tabular|b"</span><span class="p">,</span> <span class="p">&</span><span class="n" style="color: #333;">tabular</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="d"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="d">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="d">            <span class="n" style="color: #333;">printUsage</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -118,19 +128,19 @@ int flagstat_main(string[] args) {</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="d">        <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="d">        </span>

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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC130" class="line" lang="d">        <span class="k" style="font-weight: 600;">scope</span><span class="p">(</span><span class="n" style="color: #333;">exit</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"in total (QC-passed reads + QC-failed reads)"</span><span class="p">,</span> <span class="n" style="color: #333;">reads</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"secondary"</span><span class="p">,</span> <span class="n" style="color: #333;">secondary</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"supplementary"</span><span class="p">,</span> <span class="n" style="color: #333;">supplementary</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"duplicates"</span><span class="p">,</span> <span class="n" style="color: #333;">dup</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"mapped"</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">,</span> <span class="n" style="color: #333;">reads</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"paired in sequencing"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"read1"</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"read2"</span><span class="p">,</span> <span class="n" style="color: #333;">second</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"properly paired"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_good</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with itself and mate mapped"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_map</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

131

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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"singletons"</span><span class="p">,</span> <span class="n" style="color: #333;">single</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

132

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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with mate mapped to a different chr"</span><span class="p">,</span> <span class="n" style="color: #333;">diff_chr</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with mate mapped to a different chr (mapQ>=5)"</span><span class="p">,</span> <span class="n" style="color: #333;">diff_high</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"in total (QC-passed reads + QC-failed reads)"</span><span class="p">,</span> <span class="n" style="color: #333;">reads</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"secondary"</span><span class="p">,</span> <span class="n" style="color: #333;">secondary</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"supplementary"</span><span class="p">,</span> <span class="n" style="color: #333;">supplementary</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"duplicates"</span><span class="p">,</span> <span class="n" style="color: #333;">dup</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"mapped"</span><span class="p">,</span> <span class="n" style="color: #333;">mapped</span><span class="p">,</span> <span class="n" style="color: #333;">reads</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC136" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"paired in sequencing"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC137" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"read1"</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC138" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"read2"</span><span class="p">,</span> <span class="n" style="color: #333;">second</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"properly paired"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_good</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC140" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with itself and mate mapped"</span><span class="p">,</span> <span class="n" style="color: #333;">pair_map</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC141" class="line" lang="d">            <span class="n" style="color: #333;">writeParamWithPercentage</span><span class="p">(</span><span class="s" style="color: #d14;">"singletons"</span><span class="p">,</span> <span class="n" style="color: #333;">single</span><span class="p">,</span> <span class="n" style="color: #333;">pair_all</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with mate mapped to a different chr"</span><span class="p">,</span> <span class="n" style="color: #333;">diff_chr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" 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="d">            <span class="n" style="color: #333;">writeParam</span><span class="p">(</span><span class="s" style="color: #d14;">"with mate mapped to a different chr (mapQ>=5)"</span><span class="p">,</span> <span class="n" style="color: #333;">diff_high</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tabular</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="d">        <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC145" class="line" lang="d">    <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">Throwable</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="d">        <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">);</span></span>

</pre>

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</li>

<li id="3b3ae0b610f6ae26ed107e183c7ee027e957b1ed">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#3b3ae0b610f6ae26ed107e183c7ee027e957b1ed"><strong>sambamba/main.d</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,7 +83,7 @@ For bug reports and feature requests see</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printVersion</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba "</span> <span class="p">~</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">~</span> <span class="s" style="color: #d14;">" by Artem Tarasov and Pjotr Prins (C) 2012-202<span class="idiff left right">0</span>"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba "</span> <span class="p">~</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">~</span> <span class="s" style="color: #d14;">" by Artem Tarasov and Pjotr Prins (C) 2012-202<span class="idiff left right">1</span>"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"    LDC "</span> <span class="p">~</span> <span class="n" style="color: #333;">LDC_VERSION_STRING</span> <span class="p">~</span> <span class="s" style="color: #d14;">" / DMD "</span> <span class="p">~</span> <span class="n" style="color: #333;">DMD_VERSION_STRING</span> <span class="p">~</span></span>

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC88" class="line" lang="d">     <span class="s" style="color: #d14;">" / LLVM"</span> <span class="p">~</span> <span class="n" style="color: #333;">LLVM_VERSION_STRING</span> <span class="p">~</span> <span class="s" style="color: #d14;">" / bootstrap "</span> <span class="p">~</span> <span class="n" style="color: #333;">BOOTSTRAP_VERSION_STRING</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">();</span></span>

</pre>

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<br>

</li>

<li id="b888d326ed4b8a8c518a69a5de5f0ae9bc642ef9">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#b888d326ed4b8a8c518a69a5de5f0ae9bc642ef9"><strong>sambamba/markdup.d</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1246,37 +1246,40 @@ int markdup_main(string[] args) {</td>

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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="d">        <span class="n" style="color: #333;">InputRange</span><span class="p">!</span><span class="n" style="color: #333;">IndexedBamRead</span> <span class="n" style="color: #333;">reads</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="d">        <span class="k" style="font-weight: 600;">shared</span><span class="p">(</span><span class="n" style="color: #333;">ProgressBar</span><span class="p">)</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="d"></span>

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<pre style="margin: 0;">-<span id="LC1249" class="line" lang="d">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initInputs</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="d">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initInputs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">MultiBamReader</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bamreader</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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

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<td class="new_line diff-line-num" 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

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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="d">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(!</span><span class="n" style="color: #333;">show_progress</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num 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">

1251

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<td class="new_line diff-line-num 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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<pre style="margin: 0;">-<span id="LC1251" class="line" lang="d">                <span class="n" style="color: #333;">reads</span> <span class="p">=</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">withIndices</span><span class="p">.</span><span class="n" style="color: #333;">inputRangeObject</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1251

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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="d">                <span class="n" style="color: #333;">reads</span> <span class="p">=</span> <span class="n" style="color: #333;">bam<span class="idiff left right">reader</span></span><span class="p">.</span><span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">withIndices</span><span class="p">.</span><span class="n" style="color: #333;">inputRangeObject</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="d">            <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="d">                <span class="n" style="color: #333;">bar</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="k" style="font-weight: 600;">shared</span><span class="p">(</span><span class="n" style="color: #333;">ProgressBar</span><span class="p">)();</span></span>

</pre>

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<td class="old_line diff-line-num old" 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

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

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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="d">                <span class="n" style="color: #333;">reads</span> <span class="p">=</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">readsWithProgress</span><span class="p">((</span><span class="k" style="font-weight: 600;">lazy</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span> <span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1255

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

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<pre style="margin: 0;">-<span id="LC1255" class="line" lang="d">                                              <span class="p">()</span> <span class="p">{</span> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span> <span class="p">}).</span><span class="n" style="color: #333;">withIndices</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1256

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

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<pre style="margin: 0;">-<span id="LC1256" class="line" lang="d">                           <span class="p">.</span><span class="n" style="color: #333;">inputRangeObject</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1254

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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="d">                <span class="n" style="color: #333;">reads</span> <span class="p">=</span> <span class="n" style="color: #333;">bamreader</span><span class="p">.</span><span class="n" style="color: #333;">readsWithProgress</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1255

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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="d">                          <span class="p">(</span><span class="k" style="font-weight: 600;">lazy</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span> <span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1256

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

<pre style="margin: 0;">+<span id="LC1256" class="line" lang="d">                          <span class="p">()</span> <span class="p">{</span> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span> <span class="p">})</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1257

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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="d">                        <span class="p">.</span><span class="n" style="color: #333;">withIndices</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1258

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

<pre style="margin: 0;">+<span id="LC1258" class="line" lang="d">                        <span class="p">.</span><span class="n" style="color: #333;">inputRangeObject</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1259

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

<pre style="margin: 0;"> <span id="LC1259" class="line" lang="d">            <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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

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<td class="new_line diff-line-num" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1260

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

<pre style="margin: 0;"> <span id="LC1260" class="line" lang="d">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1259

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<td class="new_line diff-line-num" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1261

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

<pre style="margin: 0;"> <span id="LC1261" class="line" lang="d"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" 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="new_line diff-line-num old" 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">

</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="d">        <span class="n" style="color: #333;">initInputs</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1262

</td>

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

<pre style="margin: 0;">+<span id="LC1262" class="line" lang="d">        <span class="n" style="color: #333;">initInputs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">bam</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1261

</td>

<td class="new_line diff-line-num" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1263

</td>

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

<pre style="margin: 0;"> <span id="LC1263" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">dup_idx_storage</span> <span class="p">=</span> <span class="n" style="color: #333;">getDuplicateOffsets</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">,</span> <span class="n" style="color: #333;">rg_index</span><span class="p">,</span> <span class="n" style="color: #333;">taskPool</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1262

</td>

<td class="new_line diff-line-num" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1264

</td>

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

<pre style="margin: 0;"> <span id="LC1264" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1263

</td>

<td class="new_line diff-line-num" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1265

</td>

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

<pre style="margin: 0;"> <span id="LC1265" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">elapsed</span> <span class="p">=</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1264

</td>

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

<pre style="margin: 0;"> <span id="LC1266" class="line" lang="d">        <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"collected list of positions in "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"minutes"</span><span class="p">,</span><span class="s" style="color: #d14;">" min "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"seconds"</span> <span class="p">%</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="s" style="color: #d14;">" sec"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1265

</td>

<td class="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC1267" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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="new_line diff-line-num" 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

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

<pre style="margin: 0;"> <span id="LC1268" class="line" lang="d">        <span class="c1" style="color: #998; font-style: italic;">// marking or removing duplicates</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1267

</td>

<td class="new_line diff-line-num old" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1267" class="line" lang="d">        <span class="n" style="color: #333;">bam</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MultiBamReader</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="p">..</span> <span class="p">$-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span>  <span class="c1" style="color: #998; font-style: italic;">// FIXME: initialized twice</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1268

</td>

<td class="new_line diff-line-num old" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1268" class="line" lang="d">        <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">setBufferSize</span><span class="p">(</span><span class="n" style="color: #333;">io_buffer_size</span> <span class="p">/</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">-</span> <span class="mi" style="color: #099;">2</span><span class="p">));</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1269

</td>

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

<pre style="margin: 0;">+<span id="LC1269" class="line" lang="d">        <span class="n" style="color: #333;">bam</span> <span class="p">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1270

</td>

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

<pre style="margin: 0;">+<span id="LC1270" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">bam2</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MultiBamReader</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="p">..</span> <span class="p">$-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1271

</td>

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

<pre style="margin: 0;">+<span id="LC1271" class="line" lang="d">        <span class="n" style="color: #333;">bam2</span><span class="p">.</span><span class="n" style="color: #333;">setBufferSize</span><span class="p">(</span><span class="n" style="color: #333;">io_buffer_size</span> <span class="p">/</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">-</span> <span class="mi" style="color: #099;">2</span><span class="p">));</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1269

</td>

<td class="new_line diff-line-num" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1272

</td>

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

<pre style="margin: 0;"> <span id="LC1272" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">out_stream</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BufferedFile</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[$-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">FileMode</span><span class="p">.</span><span class="n" style="color: #333;">OutNew</span><span class="p">,</span> <span class="n" style="color: #333;">io_buffer_size</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1270

</td>

<td class="new_line diff-line-num" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1273

</td>

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

<pre style="margin: 0;"> <span id="LC1273" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">writer</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BamWriter</span><span class="p">(</span><span class="n" style="color: #333;">out_stream</span><span class="p">,</span> <span class="n" style="color: #333;">compression_level</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1271

</td>

<td class="new_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1274

</td>

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

<pre style="margin: 0;"> <span id="LC1274" class="line" lang="d">        <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">setFilename</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[$-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1272

</td>

<td class="new_line diff-line-num" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1275

</td>

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

<pre style="margin: 0;"> <span id="LC1275" class="line" lang="d">        <span class="k" style="font-weight: 600;">scope</span><span class="p">(</span><span class="n" style="color: #333;">exit</span><span class="p">)</span> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1273

</td>

<td class="new_line diff-line-num old" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1273" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">header</span> <span class="p">=</span> <span class="n" style="color: #333;">addPG</span><span class="p">(</span><span class="s" style="color: #d14;">"markdup"</span><span class="p">,</span> <span class="n" style="color: #333;">unparsed_args</span><span class="p">,</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1276

</td>

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

<pre style="margin: 0;">+<span id="LC1276" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">header</span> <span class="p">=</span> <span class="n" style="color: #333;">addPG</span><span class="p">(</span><span class="s" style="color: #d14;">"markdup"</span><span class="p">,</span> <span class="n" style="color: #333;">unparsed_args</span><span class="p">,</span> <span class="n" style="color: #333;">bam<span class="idiff left right">2</span></span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1274

</td>

<td class="new_line diff-line-num" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1277

</td>

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

<pre style="margin: 0;"> <span id="LC1277" class="line" lang="d">        <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeSamHeader</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1275

</td>

<td class="new_line diff-line-num old" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1275" class="line" lang="d">        <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeReferenceSequenceInfo</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">reference_sequences</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1278

</td>

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

<pre style="margin: 0;">+<span id="LC1278" class="line" lang="d">        <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeReferenceSequenceInfo</span><span class="p">(</span><span class="n" style="color: #333;">bam<span class="idiff left right">2</span></span><span class="p">.</span><span class="n" style="color: #333;">reference_sequences</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1276

</td>

<td class="new_line diff-line-num" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1279

</td>

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

<pre style="margin: 0;"> <span id="LC1279" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1277

</td>

<td class="new_line diff-line-num" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1280

</td>

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

<pre style="margin: 0;"> <span id="LC1280" class="line" lang="d">        <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="n" style="color: #333;">remove_duplicates</span> <span class="p">?</span> <span class="s" style="color: #d14;">"removing"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"marking"</span><span class="p">,</span> <span class="s" style="color: #d14;">" duplicates..."</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1278

</td>

<td class="new_line diff-line-num" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1281

</td>

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

<pre style="margin: 0;"> <span id="LC1281" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1279

</td>

<td class="new_line diff-line-num old" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1279" class="line" lang="d">        <span class="n" style="color: #333;">initInputs</span><span class="p">();</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1282

</td>

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

<pre style="margin: 0;">+<span id="LC1282" class="line" lang="d">        <span class="n" style="color: #333;">initInputs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">bam2</span></span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1280

</td>

<td class="new_line diff-line-num" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1283

</td>

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

<pre style="margin: 0;"> <span id="LC1283" class="line" lang="d"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1281

</td>

<td class="new_line diff-line-num" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1284

</td>

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

<pre style="margin: 0;"> <span id="LC1284" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">indices</span> <span class="p">=</span> <span class="n" style="color: #333;">dup_idx_storage</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1282

</td>

<td class="new_line diff-line-num" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1285

</td>

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

<pre style="margin: 0;"> <span id="LC1285" class="line" lang="d"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b5a32146659405cf1e2a8a45e9e3b9043c26a363">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#b5a32146659405cf1e2a8a45e9e3b9043c26a363"><strong>sambamba/pileup.d</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="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -749,4 +749,5 @@ int pileup_main(string[] args) {</td>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

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

<pre style="margin: 0;"> <span id="LC749" class="line" lang="d">          <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

</td>

<td class="new_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

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

<pre style="margin: 0;"> <span id="LC750" class="line" lang="d">        <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

</td>

<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

</td>

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

<pre style="margin: 0;"> <span id="LC751" class="line" lang="d">    <span class="p">}</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

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<pre style="margin: 0;">+<span id="LC752" class="line" lang="d">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

</td>

<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

</td>

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

<pre style="margin: 0;"> <span id="LC753" class="line" lang="d"><span class="p">}</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a2dfc645061c612393c9e78b784b01f62f7a0e42">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#a2dfc645061c612393c9e78b784b01f62f7a0e42"><strong>test/benchmark/stats.org</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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,6 +7,38 @@ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00100/alignment/HG00</td>

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

7

</td>

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

7

</td>

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

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

</pre>

</td>

</tr>

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

8

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

8

</td>

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

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

</pre>

</td>

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

9

</td>

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

9

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

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

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">Processing an 841Mb BAM file.</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

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

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

</pre>

</td>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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">*** AMD Ryzen 7 3700X 8-Core Processor</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">#+BEGIN_SRC</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">time ./bin/sambamba-0.8.1-pre1 HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam > /dev/null</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">sambamba 0.8.1-pre1</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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"> by Artem Tarasov and Pjotr Prins (C) 2012-2021</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">real    0m1.398s</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">user    0m16.589s</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">sys     0m0.240s</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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"></span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" 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="plaintext">time ./bin/sambamba-0.8.1-pre1 sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">sambamba 0.8.1-pre1</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> by Artem Tarasov and Pjotr Prins (C) 2012-2021</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

30

</td>

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">real    0m9.151s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

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

31

</td>

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">user    2m5.779s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="plaintext">sys     0m3.101s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="plaintext">time ./bin/sambamba-0.8.1-pre1 markdup HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.sorted.bam dedup.bam</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="plaintext"> by Artem Tarasov and Pjotr Prins (C) 2012-2021</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="plaintext">    LDC 1.26.0 / DMD v2.096.1 / LLVM9.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="plaintext">real    0m11.319s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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

</td>

<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="plaintext">user    1m47.719s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="plaintext">sys     0m4.070s</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="plaintext">#+END_SRC</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

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

42

</td>

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

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">*** 4x Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz (hyperthreaded)</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

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

43

</td>

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

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">**** sambamba 0.6.8-pre3</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

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

44

</td>

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3708ce0a178d356e1f2b2d1b351aeb02556a5a7a">

<a href="https://salsa.debian.org/med-team/sambamba/-/commit/12c7a3befb2326f94d108bf8bc2fb25cf924450d#3708ce0a178d356e1f2b2d1b351aeb02556a5a7a"><strong>test/test_suite.sh</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ sambamba=$1</td>

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

5

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$sambamba</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

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

6

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

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nv" style="color: #008080;">sambamba</span><span class="o" style="font-weight: 600;">=</span>./bin/sambamba</span>

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

7

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">opts</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-q"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="nv" style="color: #008080;">opts</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-q<span class="idiff left right"> --DRT-testmode=run-main</span>"</span></span>

</pre>

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

9

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">outdir</span><span class="o" style="font-weight: 600;">=</span>output</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$outdir</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); 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="207" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -207,6 +207,12 @@ testIssue356(){</td>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="shell">    assertEquals 0 <span class="nv" style="color: #008080;">$?</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="shell">testIssue421<span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" 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="shell">    <span class="c" style="color: #998; font-style: italic;"># sambamba-markdup: not enough data in stream https://github.com/biod/sambamba/issues/421</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

212

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">cat test</span>/issue_204.bam | <span class="nv" style="color: #008080;">$sambamba</span> <span class="nv" style="color: #008080;">$opts</span> markdup /dev/stdin test.bam 2> /dev/null</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="shell">    <span class="c" style="color: #998; font-style: italic;"># assertEquals 0 $?  Disable test until we have a single pass, see issue 421</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

215

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

210

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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

216

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="shell">testFastaIndex<span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

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217

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="shell">    <span class="c" style="color: #998; font-style: italic;"># check input and output are from here: http://www.htslib.org/doc/faidx.html</span></span>

</pre>

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212

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<td class="new_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

218

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="shell">    <span class="nv" style="color: #008080;">$sambamba</span> <span class="nv" style="color: #008080;">$opts</span> index <span class="nt" style="color: #000080;">-F</span> <span class="nb" style="color: #0086b3;">test</span>/test.fasta <span class="nv" style="color: #008080;">$outdir</span>/res.fai</span>

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