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GitLab

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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151">9e85e528</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-04-26T15:06:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.3+dfsg</pre>

</li>

</ul>

<h4>14 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#b5b096f958319b1c7782c800c78c4c358a58d709">

<span class="deleted-file">

−

TODO.md

</span>

</a>

</li>

<li class="file-stats">

<a href="#f8b8c04fcf7e182d3a4d9ab548e1053c614a2924">

docs/CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#f42f784781b2e42288e16f3e7bebb6e136b429fa">

docs/algorithm.rst

</a>

</li>

<li class="file-stats">

<a href="#254a2da7a740675e537439eb88e32083b9ea4771">

docs/conf.py

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<li class="file-stats">

<a href="#bfbf5db79efe6595bb859be861e6cdcadaa28003">

docs/gitversion.py

</a>

</li>

<li class="file-stats">

<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">

docs/index.rst

</a>

</li>

<li class="file-stats">

<a href="#f97da550d947325bcdd26b494d8da4c0b7c5769e">

<span class="new-file">

+

docs/tutorial.rst

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</a>

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<li class="file-stats">

<a href="#2ef0e146a333971ec0aad570ca7ea142a405edcb">

docs/usage.rst

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<li class="file-stats">

<a href="#efb8fd1a31cb69a1b8550f51972779d152196b35">

src/axe.c

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<li class="file-stats">

<a href="#55b7249702f08a10ce0cd4b5d02b624cbbc887a0">

src/axe.h

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<li class="file-stats">

<a href="#e5d9b80ab0ae13bec96749fe714a5eb21738a3a5">

src/axe_config.h.in

</a>

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<li class="file-stats">

<a href="#3a576e09615c0e19842e5f3ac31e858c9ae7fe41">

src/main.c

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<li class="file-stats">

<a href="#c62459b166a334e6529175340eedeee6977df0ca">

tests/CMakeLists.txt

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<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ existing de-multiplexers. Unscientific trials show AXE processes more than</td>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Warning**</span>: Axe has not yet been comprehensively tested. However, in the</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">spirit of "release early and often", here it is.</span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Tests:</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"> </span>Tests:</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">| TravisCI          | <span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/kdmurray91/axe.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/kdmurray91/axe) |</span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">| ----------------- | --- |</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,23 +97,11 @@ Full documentation, including a basic description of the algorithm, is hosted</td>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown">at https://axe-demultiplexer.readthedocs.org/en/latest/ .</span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="gh" style="color: #999;">Implementation Progress:</span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------</span></span>

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

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;">x</span><span class="p">]</span> Single ended read de-multiplexing</span>

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</tr>

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<td class="diff-line-num old old_line" 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

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;">x</span><span class="p">]</span> Interleaved/Paired input and output with single-ended de-multiplexing</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;">x</span><span class="p">]</span> Combinatorial de-multiplexing</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;"> </span><span class="p">]</span> CLI integration tests</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;"> </span><span class="p">]</span> Comprehensive <span class="sb" style="color: #d14;">`libaxe`</span> tests</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: teal;"> </span><span class="p">]</span> Comprehensive CLI tests</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="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="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="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="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown">See also TODO.md</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

</td>

<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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">

112

</td>

<td class="diff-line-num 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">

100

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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">

113

</td>

<td class="diff-line-num new_line" 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

</td>

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

<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gh" style="color: #999;">Publication</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" 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

</td>

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

</td>

<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

</td>

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown"><span class="idiff left right">A publication is coming soon, if the reviewer gods decide to smile upon us.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

</td>

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

<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="idiff left right">We have a preprint describing AXE up at http://www.biorxiv.org/content/early/2017/07/07/160606</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" 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">

105

</td>

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

<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

118

</td>

<td class="diff-line-num new_line" 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">

106

</td>

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

<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="gh" style="color: #999;">Versioning</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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">

119

</td>

<td class="diff-line-num new_line" 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">

107

</td>

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

<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b5b096f958319b1c7782c800c78c4c358a58d709">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#b5b096f958319b1c7782c800c78c4c358a58d709"><strong>TODO.md</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

1

</td>

<td class="diff-line-num new_line 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">TODO list:</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==========</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new_line 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

</tr>

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

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

</td>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">-</span> Re-read documentation; fix errors</span>

</pre>

</td>

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5

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<td class="diff-line-num new_line 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="LC5" class="line" lang="markdown"><span class="p">-</span> Exhaustive CLI tests</span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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="LC6" class="line" lang="markdown"><span class="p">-</span> Refactor trie lookups to hide all datrie operations from main body of code</span>

</pre>

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7

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<td class="diff-line-num new_line 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="LC7" class="line" lang="markdown"><span class="p">-</span> Summary info</span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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="LC8" class="line" lang="markdown"><span class="p">-</span> Valgrind integration tests - maybe a CLI flag to enable</span>

</pre>

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

9

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<td class="diff-line-num new_line 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="markdown"><span class="p">-</span> Investigate shipping the gsl functions bundled in source.</span></pre>

</td>

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</table>

<br>

</li>

<li id="f8b8c04fcf7e182d3a4d9ab548e1053c614a2924">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#f8b8c04fcf7e182d3a4d9ab548e1053c614a2924"><strong>docs/CMakeLists.txt</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -17,7 +17,7 @@ IF(SPHINXBUILD)</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cmake"> COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_COMMAND</span><span class="si" style="color: #d14;">}</span> -E remove_directory <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/doc"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake">        WORKING_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cmake">        <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cmake">    <span class="nf" style="color: #900; font-weight: 600;">ADD_CUSTOM_TARGET</span><span class="p">(</span>doc ALL DEPENDS doc_man doc_onehtml<span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake">    <span class="nf" style="color: #900; font-weight: 600;">ADD_CUSTOM_TARGET</span><span class="p">(</span>doc ALL DEPENDS doc_man doc_<span class="idiff left right">html doc_</span>onehtml<span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cmake">    <span class="nf" style="color: #900; font-weight: 600;">INSTALL</span><span class="p">(</span>FILES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/doc/man/axe.1 DESTINATION <span class="s2" style="color: #d14;">"share/man/man1"</span> RENAME <span class="s2" style="color: #d14;">"axe-demux.1"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cmake">    <span class="nf" style="color: #900; font-weight: 600;">SET_DIRECTORY_PROPERTIES</span><span class="p">(</span>PROPERTY ADDITIONAL_MAKE_CLEAN_FILES doc/<span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ELSE</span><span class="p">()</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="f42f784781b2e42288e16f3e7bebb6e136b429fa">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#f42f784781b2e42288e16f3e7bebb6e136b429fa"><strong>docs/algorithm.rst</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,17 +4,17 @@ Axe's matching algorithm</td>

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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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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Axe uses an algorithm based on longest-prefix-in-trie matching to match a</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">variable length from the start of each read against a set of 'mutated'</span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">barcod</span>es.</span>

</pre>

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

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

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">index</span>es.</span>

</pre>

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

8

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

8

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

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

</pre>

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

9

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

9

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

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

</pre>

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

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

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">While for most applications in high-throughput sequencing hamming distances are</span>

</pre>

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<td class="diff-line-num old old_line" 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

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

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">a frowned-upon metric, it is typical for HTS read <span class="idiff left right">barcod</span>es to be designed to</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">a frowned-upon metric, it is typical for HTS read <span class="idiff left right">index</span>es to be designed to</span>

</pre>

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

14

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

14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">tolerate a certain level of hamming mismatches. Given these sequences are short</span>

</pre>

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

15

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

15

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">and typically occur at the 5' end of reads, insertions and deletions rarely</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">need be considered, and the increased rate of assignment of reads with many</span>

</pre>

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<td class="diff-line-num old old_line" 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

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<td class="diff-line-num new_line 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">

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">errors is offset by the risk of falsely assigning <span class="idiff left right">barcod</span>es to an incorrect</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

17

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">errors is offset by the risk of falsely assigning <span class="idiff left right">index</span>es to an incorrect</span>

</pre>

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

18

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

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">sample. In any case, reads with more than 1-2 sequencing errors in their first</span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">several bases are likely to be poor quality, and will simply be filtered out</span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">during downstream quality control.</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,47 +22,47 @@ during downstream quality control.</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Hamming mismatch tries</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">----------------------</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Typically, reads are matched to a set of <span class="idiff left right">barcod</span>es by calculating the hamming</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">distance between the <span class="idiff left right">barcode</span>, and the first :math:`l` bases of a read for a</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">barcode of length :math:`l`. The "correct" barcode</span> is then selected by</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">recording either the <span class="idiff left right">barcode</span> with the lowest hamming distance to the read</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">(competitive matching) or by simply accepting the first <span class="idiff left right">barcode</span> with a hamming</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Typically, reads are matched to a set of <span class="idiff left right">index</span>es by calculating the hamming</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">distance between the <span class="idiff left right">index</span>, and the first :math:`l` bases of a read for a</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">index of length :math:`l`. The "correct" index</span> is then selected by</span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">recording either the <span class="idiff left right">index</span> with the lowest hamming distance to the read</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">(competitive matching) or by simply accepting the first <span class="idiff left right">index</span> with a hamming</span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">distance below a certain threshold.  These approaches are both very</span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">computationally expensive, and can have lower accuracy than the algorithm I</span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">propose. Additionally, implementations of these methods rarely handle <span class="idiff left right">barcod</span>es</span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">of differing length and combinatorial <span class="idiff left right">barcod</span>ing well, if at all.</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">propose. Additionally, implementations of these methods rarely handle <span class="idiff left right">index</span>es</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">of differing length and combinatorial <span class="idiff left right">index</span>ing well, if at all.</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Central to Axe's algorithm is the concept of hamming-mismatch tries. A trie is</span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">a N-ary tree for an N letter alphabet. In the case of high-throughput</span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">sequencing reads, we have the alphabet ``AGCT``, corresponding to the four</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">nucleotides of DNA, plus ``N``, used to represent ambiguous base calls. Instead</span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">of matching each <span class="idiff left right">barcode</span> to each read, we pre-calculate all allowable sequences</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">of matching each <span class="idiff left right">index</span> to each read, we pre-calculate all allowable sequences</span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">at each mismatch level, and store these in level-wise tries. For  example, to</span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">match to a hamming distance of 2, we create three tries: One containing all</span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"><span class="idiff left right">barcod</span>es, verbatim, and two tries where every sequence within a hamming</span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">distance of 1 and 2 of each <span class="idiff left right">barcode</span> respectively. Hereafter, these tries are</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"><span class="idiff left right">index</span>es, verbatim, and two tries where every sequence within a hamming</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">distance of 1 and 2 of each <span class="idiff left right">index</span> respectively. Hereafter, these tries are</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">referred to  as the 0, 1 and 2-mm tries, for a hamming distance (mismatch) of</span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">0, 1 and 2. Then, we find the longest prefix in each sequence read in the 0mm</span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">trie. If this prefix is not a valid leaf in the 0mm trie, we find the longest</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">prefix in the 1mm trie, and so on for all tries in ascending order. If no</span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">prefix of the read is a complete sequence in any trie, the read is assigned to</span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">an "non-<span class="idiff left right">barcod</span>ed" output file.</span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">an "non-<span class="idiff left right">index</span>ed" output file.</span>

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

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">This algorithm ensures optimal <span class="idiff left right">barcode</span> matching in many ways, but is also</span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">extremely fast. In situations with <span class="idiff left right">barcod</span>es of differing length, we ensure that</span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">the *longest* acceptable <span class="idiff left right">barcode</span> at a given hamming distance is chosen;</span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">assuming that sequence is random after the <span class="idiff left right">barcode</span>, the probability of false</span>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">This algorithm ensures optimal <span class="idiff left right">index</span> matching in many ways, but is also</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">extremely fast. In situations with <span class="idiff left right">index</span>es of differing length, we ensure that</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">the *longest* acceptable <span class="idiff left right">index</span> at a given hamming distance is chosen;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">assuming that sequence is random after the <span class="idiff left right">index</span>, the probability of false</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">assignments using this method is low. We also ensure that short perfect matches</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">are preferred to longer inexact matches, as we firstly only consider <span class="idiff left right">barcod</span>es</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">with no error, then 1 error, and so on. This ensures that reads with <span class="idiff left right">barcod</span>es</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">are preferred to longer inexact matches, as we firstly only consider <span class="idiff left right">index</span>es</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">with no error, then 1 error, and so on. This ensures that reads with <span class="idiff left right">index</span>es</span>

</pre>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">that are followed by random sequence that happens to inexactly match a longer</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"><span class="idiff left right">barcode in the set are not falsely assigned to this longer barcode</span>.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"><span class="idiff left right">index in the set are not falsely assigned to this longer index</span>.</span>

</pre>

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

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

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">The speed of this algorithm is largely due to the constant time matching</span>

</pre>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">algorithm with respect to the number of <span class="idiff left right">barcod</span>es to match. The time taken to</span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">match each read is proportional instead to the length of the <span class="idiff left right">barcod</span>es, as for a</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"><span class="idiff left right">barcode</span> of length :math:`l`, at most :math:`l + 1` trie level descents are</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">algorithm with respect to the number of <span class="idiff left right">index</span>es to match. The time taken to</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">match each read is proportional instead to the length of the <span class="idiff left right">index</span>es, as for a</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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="plaintext"><span class="idiff left right">index</span> of length :math:`l`, at most :math:`l + 1` trie level descents are</span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">required to find an entry in the trie. As this length is more-or-less constant</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">and small, the overall complexity of axe's algorithm is :math:`O(n)` for</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">:math:`n` reads, as opposed to :math:`O(nm)` for :math:`n` reads and :math:`m`</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"><span class="idiff left right">barcod</span>es as is typical for traditional matching algorithms</span></pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"><span class="idiff left right">index</span>es as is typical for traditional matching algorithms</span></pre>

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<br>

</li>

<li id="254a2da7a740675e537439eb88e32083b9ea4771">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</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">@@ -31,7 +31,7 @@ import gitversion</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ones.</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">    <span class="s" style="color: #d14;">'sphinx.ext.todo'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">    <span class="s" style="color: #d14;">'sphinx.ext.<span class="idiff left right">pn</span>gmath'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="s" style="color: #d14;">'sphinx.ext.<span class="idiff left right">im</span>gmath'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">    <span class="s" style="color: #d14;">'sphinx.ext.ifconfig'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="p">]</span></span>

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

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -188,10 +188,10 @@ htmlhelp_basename = 'axedoc'</td>

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

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="n" style="color: #333;">latex_elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The paper size ('letterpaper' or 'a4paper').</span></span>

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<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;">'papersize'</span><span class="p">:</span> <span class="s" style="color: #d14;">'a4paper'</span><span class="p">,</span></span>

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

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>'papersize': 'a4paper',</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The font size ('10pt', '11pt' or '12pt').</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;">'pointsize'</span><span class="p">:</span> <span class="s" style="color: #d14;">'11pt'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>'pointsize': '11pt',</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Additional stuff for the LaTeX preamble.</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#'preamble': '',</span></span>

</pre>

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<br>

</li>

<li id="bfbf5db79efe6595bb859be861e6cdcadaa28003">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#bfbf5db79efe6595bb859be861e6cdcadaa28003"><strong>docs/gitversion.py</strong></a>

<hr>

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

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

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># versioneer-0.13 (https://github.com/warner/python-versioneer)</span></span>

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

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

</pre>

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<td class="diff-line-num old_line" 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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># these strings will be replaced by git during git-archive</span></span>

</pre>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: 0.3.2</span>)"</span></span>

</pre>

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12

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0faf8e3e05ba45343357e0cfa6c9657cedee4cc9</span>"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: 0.3.3</span>)"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">4b985d2ac95b046e96f0a83cb98f1f5e31fa49bd</span>"</span></span>

</pre>

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

13

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># these strings are filled in when 'setup.py versioneer' creates _version.py</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">tag_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="d0153cac95479af9bfb99b746b633bc8255bb53a">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</strong></a>

<hr>

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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">@@ -7,16 +7,17 @@ Welcome to axe's documentation!</td>

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

</pre>

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

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

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

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

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Axe is a read de-multiplexer, useful in situations where sequence reads contain</span>

</pre>

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">the <span class="idiff left right">barcod</span>es that uniquely distinguish samples. Axe uses a rapid and accurate</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">the <span class="idiff left right">index</span>es that uniquely distinguish samples. Axe uses a rapid and accurate</span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">algorithm based on hamming mismatch tries to competitively match the prefix of</span>

</pre>

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

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">a sequencing read against a set of <span class="idiff left right">barcod</span>es. Axe supports combinatorial</span>

</pre>

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

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">barcod</span>ing schemes.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">a sequencing read against a set of <span class="idiff left right">index</span>es. Axe supports combinatorial</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">index</span>ing schemes.</span>

</pre>

</td>

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

14

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14

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

</pre>

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

</pre>

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

</pre>

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">.. toctree::</span>

</pre>

</td>

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<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">   :maxdepth: <span class="idiff left right">2</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">   :maxdepth: <span class="idiff left right">1</span></span>

</pre>

</td>

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

</pre>

</td>

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">   tutorial</span>

</pre>

</td>

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

</pre>

</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="f97da550d947325bcdd26b494d8da4c0b7c5769e">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#f97da550d947325bcdd26b494d8da4c0b7c5769e"><strong>docs/tutorial.rst</strong></a>

<hr>

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1

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

</pre>

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

2

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

</pre>

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

3

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

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

</pre>

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4

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

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

</pre>

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5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">In this tutorial, we'll use Axe to demultiplex some paired-end,</span>

</pre>

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6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">combinatorially-index Genotyping-by-Sequencing reads. The data for this</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">tutorial is available from figshare:</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">https://figshare.com/articles/axe-tutorial_tar/6143720 .</span>

</pre>

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9

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

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Axe should be run as the initial step of any analysis: don't use sequence QC</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">tools like AdapterRemoval or Trimmomatic before using axe, as indexes may be</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">trimmed away, or pairing information removed.</span>

</pre>

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13

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

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Step 0: Download the trial data</span>

</pre>

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

</pre>

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

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">This will download the trial data, and extract it on the fly:</span>

</pre>

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18

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

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">   curl -LS https://ndownloader.figshare.com/files/11094782 | tar xv</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Step 1: prepare a key file</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">--------------------------</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">The key file associates index sequences with sample names. A key file can be</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">prepared in a spreadsheet editor, like LibreOffice Calc, or Excel. The format</span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">is quite strict, and is described in detail in the online usage documentation.</span>

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Let's now inspect the keyfile I have provided for the tutorial.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">   head axe-keyfile.tsv</span>

</pre>

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

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Step 2: Demultiplex with Axe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">----------------------------</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">In this step, we will demultiplex our interleaved input file to per-sample</span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">interleaved output files. To see a full range of Axe's options, please run</span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">``axe-demux -h``, or inspect the online usage documentation.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">First, let's inspect the input.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">   zcat axe-tutorial.fastq.gz | head -n 8</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Then, we need to ensure that axe has somewhere to put the demultiplexed reads.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Axe outputs one file (or more, depending on pairing) per sample. Axe does so by</span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">appending the sample name to some prefix (as given by the ``-I``, ``-F``,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">and/or ``-R`` options). If this prefix is a directory, then sample fastq files</span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">will be created in that sub-directory, but the directory must exist. Let's make</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">an output directory:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">   mkdir -p output</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Now, let's demultiplex the reads!</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.. code-block:: bash</span>

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

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">   axe-demux -i axe-tutorial.fastq.gz -I output/ \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">      -c -b axe-keyfile.tsv -t demux-stats.tsv -z 1</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">The command above demultiplexes reads from ``axe-tutorial.fastq.gz`` into</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">separate files under ``output``, based on the combinatorial (``-c``)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">sample-to-index-sequence mapping described in ``axe-keyfile.tsv``, and saves a</span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">file of statistics as ``demux-stats.tsv``. Note that we have enabled</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">compression of output files using the ``-z`` option, in case you don't have</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">much disk space available. This will make Axe slightly slower.</span></pre>

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<br>

</li>

<li id="2ef0e146a333971ec0aad570ca7ea142a405edcb">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#2ef0e146a333971ec0aad570ca7ea142a405edcb"><strong>docs/usage.rst</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,15 +9,16 @@ Axe Usage</td>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  did not change.</span>

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

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Axe has several usage modes. The primary distinction is between the two</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">alternate <span class="idiff left right">barcoding schemes, single and combinatorial barcoding. Single barcode</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">matching is used when only the first read contains <span class="idiff left right">barcode</span> sequences.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Combinatorial <span class="idiff left right">barcod</span>ing is used when both reads in a read pair contain</span>

</pre>

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<td class="diff-line-num new_line 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="LC15" class="line" lang="plaintext">independent (typically different) <span class="idiff left right">barcode</span> sequences.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">alternate <span class="idiff left right">indexing schemes, single and combinatorial indexing. Single index</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">matching is used when only the first read contains <span class="idiff left right">index</span> sequences.</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Combinatorial <span class="idiff left right">index</span>ing is used when both reads in a read pair contain</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">independent (typically different) <span class="idiff left right">index</span> sequences.</span>

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">For concise reference, the command-line usage of ``axe-demux`` is reproduced</span>

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

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.. literalinclude:: usage.txt</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">   :language: text</span>

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Inputs and Outputs</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">------------------</span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,8 +38,8 @@ default) and 9, where 0 indicates plain text output (``gzopen`` mode "wT"), and</td>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">fastest and 9 is most compact.</span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">The output flags should be prefixes that are used to generate the output file</span>

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">name based on the <span class="idiff left right">barcode's (or barcode</span> pair's) ID. The names are generated as:</span>

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">``prefix`` + ``_`` + ``<span class="idiff left right">barcode</span> ID`` + ``_`` + ``read number`` + ``.extension``.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">name based on the <span class="idiff left right">index's (or index</span> pair's) ID. The names are generated as:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">``prefix`` + ``_`` + ``<span class="idiff left right">index</span> ID`` + ``_`` + ``read number`` + ``.extension``.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">The output file for reads that could not be demultiplexed is ``prefix`` + ``_``</span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">+ ``unknown`` + ``_`` + ``read number`` + ``.extension``.  The read number is</span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">omitted unless the paired read file scheme is used, and is "il" for interleaved</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">@@ -51,65 +52,65 @@ The corresponding CLI flags are:</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> - ``-r`` and ``-R``: Paired R2 file input and output.</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> - ``-i`` and ``-I``: Interleaved paired input and output.</span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">The <span class="idiff left right">barcode</span> file</span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">The <span class="idiff left right">index</span> file</span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">----------------</span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">The <span class="idiff left right">barcode</span> file is a tab-separated file with an optional header. It is</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">The <span class="idiff left right">index</span> file is a tab-separated file with an optional header. It is</span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">mandatory, and is always supplied using the ``-b`` command line flag. The exact</span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">format is dependent on <span class="idiff left right">barcod</span>ing mode, and is described further in the sections</span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">format is dependent on <span class="idiff left right">index</span>ing mode, and is described further in the sections</span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">below. If a header is present, the header line must start with either</span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">`Barcode` or ``<span class="idiff left right">barcode``, or it will be interpreted as a barcode</span> line, leading</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">`Barcode` or ``<span class="idiff left right">index``, or it will be interpreted as a index</span> line, leading</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">to a parsing error. Any line starting with ';' or '#' is ignored, allowing</span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">comments to be added in line with <span class="idiff left right">barcod</span>es. Please ensure that the software</span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">used to produce the <span class="idiff left right">barcode</span> uses ASCII encoding, and does not insert a</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">comments to be added in line with <span class="idiff left right">index</span>es. Please ensure that the software</span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">used to produce the <span class="idiff left right">index</span> uses ASCII encoding, and does not insert a</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">Byte-order Mark (BoM) as many text editors can silently use Unicode-based</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">encoding schemes. I recommend the use of</span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">`LibreOffice Calc <www.libreoffice.org>`_ (part of a free and open source</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">office suite) to generate <span class="idiff left right">barcode</span> tables; Microsoft Excel can also be used.</span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">office suite) to generate <span class="idiff left right">index</span> tables; Microsoft Excel can also be used.</span>

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

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Mismatch level selection</span>

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

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

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">Independent of <span class="idiff left right">barcode</span> mode, the ``-m`` flag is used to select the maximum</span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">allowable hamming distance between a read's prefix and a <span class="idiff left right">barcode</span> to be</span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">considered as a match. As "mutated" <span class="idiff left right">barcod</span>es must be unique, a hamming distance</span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">of one is the default as typically <span class="idiff left right">barcod</span>es are designed to differ by a hamming</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">Independent of <span class="idiff left right">index</span> mode, the ``-m`` flag is used to select the maximum</span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">allowable hamming distance between a read's prefix and a <span class="idiff left right">index</span> to be</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">considered as a match. As "mutated" <span class="idiff left right">index</span>es must be unique, a hamming distance</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">of one is the default as typically <span class="idiff left right">index</span>es are designed to differ by a hamming</span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">distance of at least two. Optionally, (using the ``-p`` flag), axe will allow</span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">selective mismatch levels, where, if clashes are observed, the <span class="idiff left right">barcode</span> will</span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">only be matched exactly. This allows one to process datasets with <span class="idiff left right">barcod</span>es that</span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">selective mismatch levels, where, if clashes are observed, the <span class="idiff left right">index</span> will</span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">only be matched exactly. This allows one to process datasets with <span class="idiff left right">index</span>es that</span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">don't have a sufficiently high distance between them.</span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">Single <span class="idiff left right">barcode</span> mode</span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Single <span class="idiff left right">index</span> mode</span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">-------------------</span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">Single <span class="idiff left right">barcode</span> mode is the default mode of operation. Barcodes are matched</span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">against read one (hereafter the forward read), and the <span class="idiff left right">barcode</span> is trimmed from</span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Single <span class="idiff left right">index</span> mode is the default mode of operation. Barcodes are matched</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">against read one (hereafter the forward read), and the <span class="idiff left right">index</span> is trimmed from</span>

</pre>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">only the forward read, unless the ``-2`` command line flag is given, in which</span>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">case a prefix the same length as the matched <span class="idiff left right">barcode</span> is also trimmed from the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">case a prefix the same length as the matched <span class="idiff left right">index</span> is also trimmed from the</span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">second or reverse read. Note that sequence of this second read is not checked</span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">before trimming.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">In single <span class="idiff left right">barcode mode, the barcode</span> file has two columns: ``Barcode`` and</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">In single <span class="idiff left right">index mode, the index</span> file has two columns: ``Barcode`` and</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">``ID``.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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

<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">Combinatorial <span class="idiff left right">barcode</span> mode</span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">Combinatorial <span class="idiff left right">index</span> mode</span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">--------------------------</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">Combinatorial <span class="idiff left right">barcode</span> mode is activated by giving the ``-c`` flag on the</span>

</pre>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">command line. Forward read <span class="idiff left right">barcod</span>es are matched against the forward read, and</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">reverse read <span class="idiff left right">barcod</span>es are matched against the reverse read. The optimal</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"><span class="idiff left right">barcodes are selected independently, and the barcode</span> pair is selected from</span>

</pre>

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

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">these two <span class="idiff left right">barcodes. The respective  barcod</span>es are trimmed from both reads; the</span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">``-2`` command line flag has no effect in combinatorial <span class="idiff left right">barcode</span> mode.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">Combinatorial <span class="idiff left right">index</span> mode is activated by giving the ``-c`` flag on the</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">command line. Forward read <span class="idiff left right">index</span>es are matched against the forward read, and</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">reverse read <span class="idiff left right">index</span>es are matched against the reverse read. The optimal</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"><span class="idiff left right">indexes are selected independently, and the index</span> pair is selected from</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">these two <span class="idiff left right">indexes. The respective  index</span>es are trimmed from both reads; the</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">``-2`` command line flag has no effect in combinatorial <span class="idiff left right">index</span> mode.</span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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="plaintext"></span>

</pre>

</td>

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

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">In combinatorial <span class="idiff left right">barcode mode, the barcode</span> file has three columns:</span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">``Barcode1``, ``Barcode2`` and ``ID``. Individual <span class="idiff left right">barcod</span>es can occur many times</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">within the forward and reverse <span class="idiff left right">barcodes, but barcode</span> pairs must be unique</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">In combinatorial <span class="idiff left right">index mode, the index</span> file has three columns:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">``Barcode1``, ``Barcode2`` and ``ID``. Individual <span class="idiff left right">index</span>es can occur many times</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">within the forward and reverse <span class="idiff left right">indexes, but index</span> pairs must be unique</span>

</pre>

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<td class="diff-line-num old_line" 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">

108

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<td class="diff-line-num new_line" 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">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">combinations.</span>

</pre>

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<td class="diff-line-num old_line" 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="LC110" class="line" lang="plaintext"></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">The Demultipexing Statistics File</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">---------------------------------</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">The Demultip<span class="idiff left right">l</span>exing Statistics File</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">---------------------------------<span class="idiff left right">-</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" 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="LC113" class="line" lang="plaintext"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">The ``-t`` option allows the output of per-sample read counts to a</span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">tab-separated file. The file will have a header describing its format, and</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">includes a line for <span class="idiff left right">unbarcoded reads</span>.</span></pre>

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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">includes a line for <span class="idiff left right">reads which could not be demultiplexed</span>.</span></pre>

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<br>

</li>

<li id="efb8fd1a31cb69a1b8550f51972779d152196b35">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#efb8fd1a31cb69a1b8550f51972779d152196b35"><strong>src/axe.c</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *       Filename:  axe.c</span></span>

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *    Description:  Demultiplex reads by 5' barcodes</span></span>

</pre>

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<td class="diff-line-num new_line 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="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">5 Kevin Murray <spam@kdmurray.id.au</span>></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">6 Kevin Murray <kdmfoss@gmail.com</span>></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *        License:  GNU GPL v3+</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This program is free software: you can redistribute it and/or modify it</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -24,6 +24,9 @@</td>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "axe.h"</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "gsl_combination.h"</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/types.h></span></span>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/stat.h></span></span>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.h></span></span>

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

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Holds the current timestamp, so we don't have to free the returned string</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * from now(). */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,16 +172,15 @@ _axe_format_outfile_path (const char *prefix, const char *id, int read,</td>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">4096</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">our_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">lastchr</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">stat</span> <span class="n" style="color: #333;">statbuff</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c">    <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c">    <span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<td class="diff-line-num new_line 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="LC180" class="line" lang="c">    <span class="n" style="color: #333;">lastchr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

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<td class="diff-line-num new_line 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="LC181" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lastchr</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">lastchr</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\\'</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">statbuff</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">S_ISDIR</span><span class="p">(</span><span class="n" style="color: #333;">statbuff</span><span class="p">.</span><span class="n" style="color: #333;">st_mode</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c">        <span class="cm" style="color: #998; font-style: italic;">/* Our prefix is a directory, don't add '_' */</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c">        <span class="n" style="color: #333;">our_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strdup</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<br>

</li>

<li id="55b7249702f08a10ce0cd4b5d02b624cbbc887a0">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#55b7249702f08a10ce0cd4b5d02b624cbbc887a0"><strong>src/axe.h</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *       Filename:  axe.h</span></span>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *    Description:  Demultiplex reads by 5' barcodes</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">5 Kevin Murray <spam@kdmurray.id.au</span>></span></span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">6 Kevin Murray <kdmfoss@gmail.com</span>></span></span>

</pre>

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

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *        License:  GNU GPL v3+</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This program is free software: you can redistribute it and/or modify it</span></span>

</pre>

</td>

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<br>

</li>

<li id="e5d9b80ab0ae13bec96749fe714a5eb21738a3a5">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#e5d9b80ab0ae13bec96749fe714a5eb21738a3a5"><strong>src/axe_config.h.in</strong></a>

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

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> *       Filename:  axe_config.h.in</span>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> *    Description:  Pull in build system definitions</span>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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"> *      Copyright:  2014-201<span class="idiff left right">5 Kevin Murray <spam@kdmurray.id.au</span>></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> *      Copyright:  2014-201<span class="idiff left right">6 Kevin Murray <kdmfoss@gmail.com</span>></span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> *        License:  GNU GPL v3+</span>

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

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

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * This program is free software: you can redistribute it and/or modify it</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3a576e09615c0e19842e5f3ac31e858c9ae7fe41">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#3a576e09615c0e19842e5f3ac31e858c9ae7fe41"><strong>src/main.c</strong></a>

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *       Filename:  axe_main.c</span></span>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *    Description:  Main loop for axe</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">5 Kevin Murray <spam@kdmurray.id.au</span>></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *      Copyright:  2014-201<span class="idiff left right">6 Kevin Murray <kdmfoss@gmail.com</span>></span></span>

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

7

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *        License:  GNU GPL v3+</span></span>

</pre>

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

8

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

9

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This program is free software: you can redistribute it and/or modify it</span></span>

</pre>

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<br>

</li>

<li id="c62459b166a334e6529175340eedeee6977df0ca">

<a href="https://salsa.debian.org/med-team/axe-demultiplexer/commit/9e85e5282ee85321838dab9e621dd6962552e151#c62459b166a334e6529175340eedeee6977df0ca"><strong>tests/CMakeLists.txt</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ IF (CMAKE_BUILD_TYPE STREQUAL "Coverage")</td>

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

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<td class="diff-line-num new_line" data-linenumber="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="cmake"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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="cmake">         <span class="c1" style="color: #998; font-style: italic;"># Capturing lcov counters and generating report</span></span>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LCOV_PATH</span><span class="si" style="color: #d14;">}</span> --rc lcov_branch_coverage=1 --directory <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/src --capture --output-file <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info</span>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LCOV_PATH</span><span class="si" style="color: #d14;">}</span> --rc lcov_branch_coverage=1 --output-file <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info --remove <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info src/<span class="idiff left right">kmlib</span>/*</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LCOV_PATH</span><span class="si" style="color: #d14;">}</span> --rc lcov_branch_coverage=1 --output-file <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info --remove <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info src/<span class="idiff left right">libqes</span>/*</span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LCOV_PATH</span><span class="si" style="color: #d14;">}</span> --rc lcov_branch_coverage=1 --output-file <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info --remove <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info src/datrie/*</span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">GENHTML_PATH</span><span class="si" style="color: #d14;">}</span> --branch-coverage -o <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info</span>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cmake">         COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_COMMAND</span><span class="si" style="color: #d14;">}</span> -E remove <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COVERAGE_OUT</span><span class="si" style="color: #d14;">}</span>.info</span>

</pre>

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