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GitLab

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<h3>

Fabian Klötzl pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c">70820b09</a></strong>

<div>

<span>by Fabian Klötzl</span>

<i>at 2021-12-30T13:21:32+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.14</pre>

</li>

</ul>

<h4>17 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#5b785a47c2276fad59c8479f07f96b491e3db561">

andi-manual.pdf

</a>

</li>

<li class="file-stats">

<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

configure.ac

</a>

</li>

<li class="file-stats">

<a href="#c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da">

docs/andi.1.in

</a>

</li>

<li class="file-stats">

<a href="#866c333caed2725512f59600c796c8e0be2b69ff">

docs/manual/andi-manual.tex

</a>

</li>

<li class="file-stats">

<a href="#23655b38096d1b45f344b98fb5d184fa57045cdb">

docs/manual/references.bib

</a>

</li>

<li class="file-stats">

<a href="#d53e5440386e36e96bb1d35d8ad8add7cfdcb87b">

libs/pfasta.c

</a>

</li>

<li class="file-stats">

<a href="#3aab6304ca2cf0f34ba9680d12c87d6b0e5cfead">

libs/pfasta.h

</a>

</li>

<li class="file-stats">

<a href="#28db630a02e8ffab6561cceefc6c8e0426b5e1b0">

scripts/_andi

</a>

</li>

<li class="file-stats">

<a href="#67e794015a01b8816bd16290e5f8538236da8245">

src/Makefile.am

</a>

</li>

<li class="file-stats">

<a href="#e4121eb35479a00bb2becf6c512563545bb34482">

src/andi.c

</a>

</li>

<li class="file-stats">

<a href="#c30c220576b993ebc2341d565eb0ff0c4a10da82">

src/global.h

</a>

</li>

<li class="file-stats">

<a href="#0f3044ba93433ecc1c927c85984cb8dc55b76b9f">

src/io.c

</a>

</li>

<li class="file-stats">

<a href="#93f5f7039d98b42c276a3759cba8ff5bea5a2d7e">

src/model.c

</a>

</li>

<li class="file-stats">

<a href="#91f1a287183fa08d7cffd01580a5050be8989762">

src/model.h

</a>

</li>

<li class="file-stats">

<a href="#01a89d148d2434a88bba979e1ef4be45506178a5">

test/Makefile.am

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@ language: cpp</td>

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2

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2

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

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

</pre>

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

3

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

3

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

</pre>

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

4

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

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>

</pre>

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

</td>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>

</pre>

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

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

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">amd64</span></span>

</pre>

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

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

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">ppc64le</span></span>

</pre>

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

5

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<td class="new_line diff-line-num" data-linenumber="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="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>

</pre>

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6

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

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

7

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml">  <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ For Debian and Ubuntu:</td>

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

</pre>

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16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;">    sudo apt-get install andi</span></span>

</pre>

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

17

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

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

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

</pre>

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

18

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

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">For OS<span class="idiff left right"> X</span> with Homebrew:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

18

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">For <span class="idiff left right">mac</span>OS with Homebrew:</span>

</pre>

</td>

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

19

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="sb" style="color: #d14;">    brew tap brewsci/bio</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="sb" style="color: #d14;">    brew install andi</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,7 +68,7 @@ The release of this software is accompanied by a paper from [Haubold et al.](htt</td>

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

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown">Copyright © 2014 - 202<span class="idiff left right">0</span> Fabian Klötzl  </span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">Copyright © 2014 - 202<span class="idiff left right">1</span> Fabian Klötzl  </span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">License GPLv3+: GNU GPL version 3 or later.</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown">This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at <span class="nv" style="color: #008080;"><http://gnu.org/licenses/gpl.html></span>.</span>

</pre>

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<br>

</li>

<li id="5b785a47c2276fad59c8479f07f96b491e3db561">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#5b785a47c2276fad59c8479f07f96b491e3db561"><strong>andi-manual.pdf</strong></a>

<hr>

No preview for this file type

<br>

</li>

<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT([andi], [0.1<span class="idiff left right">3</span>])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT([andi], [0.1<span class="idiff left right">4</span>])</span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall foreign])</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_CONFIG_MACRO_DIR([m4])</span>

</pre>

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<br>

</li>

<li id="c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da"><strong>docs/andi.1.in</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ Use this mode if each of your \fIFASTA\fR files represents one assembly with num</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">In multithreaded mode, \fBandi\fR requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost.</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">\fB\-m\fR \fIMODEL\fR, \fB\-\-model\fR=\fIMODEL\fR</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">Set the nucleotide evolution model to one of 'Raw', 'JC', <span class="idiff left right">or </span>'Kimura'. By default the Jukes-Cantor correction is used.</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Set the nucleotide evolution model to one of 'Raw', 'JC', 'Kimura'<span class="idiff left right">, or 'LogDet'</span>. By default the Jukes-Cantor correction is used.</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">.TP</span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">\fB\-p\fR \fIFLOAT\fR</span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Significance of an anchor; default: 0.025.</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -48,7 +48,7 @@ Prints the synopsis and an explanation of available options.</td>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">\fB\-\-version\fR</span>

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Outputs version information and acknowledgments.</span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">Copyright \(co 2014 - 202<span class="idiff left right">0</span> Fabian Klötzl</span>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Copyright \(co 2014 - 202<span class="idiff left right">1</span> Fabian Klötzl</span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">License GPLv3+: GNU GPL version 3 or later.</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">This is free software: you are free to change and redistribute it.</span>

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<br>

</li>

<li id="866c333caed2725512f59600c796c8e0be2b69ff">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#866c333caed2725512f59600c796c8e0be2b69ff"><strong>docs/manual/andi-manual.tex</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>caption<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>subcaption<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>xspace<span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="tex"><span class="k" style="font-weight: 600;">\usepackage</span><span class="p">{</span>microtype<span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="tex"><span class="k" style="font-weight: 600;">\bibliographystyle</span><span class="p">{</span>alpha<span class="p">}</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -134,16 +135,16 @@ To build \andi from source, download the latest \href{https://github.com/EvolBio</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="tex">Once you have downloaded the package, unzip it and change into the newly created directory. </span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{lstlisting}</span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  tar -xzvf andi-0.1<span class="idiff left right">2</span>.tar.gz</span></span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  cd andi-0.1<span class="idiff left right">2</span></span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  tar -xzvf andi-0.1<span class="idiff left right">4</span>.tar.gz</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  cd andi-0.1<span class="idiff left right">4</span></span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> Now build and install <span class="k" style="font-weight: 600;">\andi</span>.</span>

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

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{lstlisting}</span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  ./configure</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  make</span></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  sudo make install</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="tex">~/andi-0.1<span class="idiff left right">4</span> <span class="c" style="color: #998; font-style: italic;">%  ./configure</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="tex">~/andi-0.1<span class="idiff left right">4</span> <span class="c" style="color: #998; font-style: italic;">%  make</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="tex">~/andi-0.1<span class="idiff left right">4</span> <span class="c" style="color: #998; font-style: italic;">%  sudo make install</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> This installs <span class="k" style="font-weight: 600;">\andi</span> for all users on your system. If you do not have root privileges, you will find a working copy of <span class="k" style="font-weight: 600;">\andi</span> in the <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">src</span><span class="p">$</span> subdirectory. For the rest of this documentation, it is assumed, that <span class="k" style="font-weight: 600;">\andi</span> is in your <span class="k" style="font-weight: 600;">\textdollar\lstinline</span>!PATH!.</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">@@ -151,15 +152,16 @@ Once you have downloaded the package, unzip it and change into the newly created</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="tex">Now <span class="k" style="font-weight: 600;">\andi</span> should be ready for use. Try invoking the help.</span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{lstlisting}</span></span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="tex">~/andi-0.12 <span class="c" style="color: #998; font-style: italic;">%  Usage: andi [OPTIONS...] FILES...</span></span>

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

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="tex">  FILES... can be any sequence of FASTA files.</span>

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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="tex">  Use '-' as file name to read from stdin.</span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="tex">~/andi-0.14 <span class="c" style="color: #998; font-style: italic;">%  ~/andi</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="tex">Usage: andi [OPTIONS...] FILES...</span>

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="tex">  FILES... can be any sequence of FASTA files.</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="tex">  Use '-' as file name to read from stdin.</span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="tex">  -b, --bootstrap=INT  Print additional bootstrap matrices</span>

</pre>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="tex">      --file-of-filenames=FILE  Read additional filenames from FILE; one per line</span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="tex">  -j, --join           Treat all sequences from one file as a single genome</span>

</pre>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="tex">  -l, --low-memory     Use less memory at the cost of speed</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="tex">  -m, --model=MODEL    Pick an evolutionary model of 'Raw', 'JC', 'Kimura'; default: JC</span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="tex">  -m, --model=MODEL    Pick an evolutionary model of 'Raw', 'JC', 'Kimura'<span class="idiff left right">, 'LogDet'</span>; default: JC</span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="tex">  -p FLOAT             Significance of an anchor; default: 0.025</span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="tex">      --progress=WHEN  Print a progress bar 'always', 'never', or 'auto'; default: auto</span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="tex">  -t, --threads=INT    Set the number of threads; by default, all processors are used</span>

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

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="tex">In the above examples the runtime dropped from <span class="k" style="font-weight: 600;">\SI</span><span class="p">{</span>0.613<span class="p">}{</span><span class="k" style="font-weight: 600;">\second</span><span class="p">}</span>, to <span class="k" style="font-weight: 600;">\SI</span><span class="p">{</span>0.362<span class="p">}{</span><span class="k" style="font-weight: 600;">\second</span><span class="p">}</span> using two threads. Giving <span class="k" style="font-weight: 600;">\andi</span> more threads than input genomes leads to no further speed improvement. <span class="k" style="font-weight: 600;">\,</span> The other important option is <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">join</span><span class="p">$</span> (see Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sec:join<span class="p">}</span>).</span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="tex">By default, the distances computed by <span class="k" style="font-weight: 600;">\andi</span> are <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>Jukes-Cantor<span class="p">}</span> corrected <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>jukescantor<span class="p">}</span>. Other evolutionary models are also implemented (Kimura, raw). The <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">model</span><span class="p">$</span> parameter can be used to switch between them.</span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="tex">By default, the distances computed by <span class="k" style="font-weight: 600;">\andi</span> are <span class="k" style="font-weight: 600;">\emph</span><span class="p">{</span>Jukes-Cantor<span class="p">}</span> corrected <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>jukescantor<span class="p">}</span>. Other evolutionary models are also implemented (Kimura<span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">\cite</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">kimura</span><span class="p"><span class="idiff">}</span></span><span class="idiff">, LogDet </span><span class="k" style="font-weight: 600;"><span class="idiff">\cite</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">logdet</span><span class="p"><span class="idiff right">}</span></span>, raw). The <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">model</span><span class="p">$</span> parameter can be used to switch between them.</span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="tex">Since version 0.9.4 <span class="k" style="font-weight: 600;">\andi</span> includes a bootstrapping method. It can be activated via the <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">bootstrap</span><span class="p">$</span> or <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">b</span><span class="p">$</span> switch. This option takes a numeric argument representing the number of matrices to create. The output can then be piped into <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>phylip<span class="p">}</span>. For more information on computing support values from distance matrices see <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>afra<span class="p">}</span>.</span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection*</span><span class="p">{</span>Too Short Sequence<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> was designed for big data sets of whole genomes. On short sequences the distance estimates are inaccurate. Use a<span class="idiff left right">n</span> multiple sequence alignment instead.</span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> was designed for big data sets of whole genomes. On short sequences the distance estimates are inaccurate. Use a multiple sequence alignment instead.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection*</span><span class="p">{</span>Too Long Sequence<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="tex"></span>

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</li>

<li id="23655b38096d1b45f344b98fb5d184fa57045cdb">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#23655b38096d1b45f344b98fb5d184fa57045cdb"><strong>docs/manual/references.bib</strong></a>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="bibtex">  <span class="na" style="color: #008080;">DOI</span> <span class="p">=</span> <span class="s" style="color: #d14;">{10.3390/life6010011}</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="bibtex"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="bibtex"></span>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="bibtex"><span class="nc" style="color: #458; font-weight: 600;">@article</span><span class="p">{</span><span class="nl">logdet</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="bibtex">  <span class="na" style="color: #008080;">AUTHOR</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Lockhart, P.J. and M.A. Steel and M.D. Hendy and D. Penny}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="bibtex">  <span class="na" style="color: #008080;">TITLE</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Recovering Evolutionary Trees under a More Realistic Model of Sequence Evolution}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="bibtex">  <span class="na" style="color: #008080;">JOURNAL</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Molecular Biology and Evolution}</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="bibtex">  <span class="na" style="color: #008080;">VOLUME</span> <span class="p">=</span> <span class="s" style="color: #d14;">{11}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="bibtex">  <span class="na" style="color: #008080;">YEAR</span> <span class="p">=</span> <span class="s" style="color: #d14;">{1994}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="bibtex">  <span class="na" style="color: #008080;">NUMBER</span> <span class="p">=</span> <span class="s" style="color: #d14;">{4}</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="bibtex">  <span class="na" style="color: #008080;">PAGES</span> <span class="p">=</span> <span class="s" style="color: #d14;">{605-612}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="bibtex">  <span class="na" style="color: #008080;">DOI</span> <span class="p">=</span> <span class="s" style="color: #d14;">{10.1093/oxfordjournals.molbev.a040136}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="bibtex"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="bibtex"></span>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="bibtex"><span class="nc" style="color: #458; font-weight: 600;">@article</span><span class="p">{</span><span class="nl">kimura</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="bibtex">  <span class="na" style="color: #008080;">AUTHOR</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Kimura, M.}</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="bibtex">  <span class="na" style="color: #008080;">TITLE</span> <span class="p">=</span> <span class="s" style="color: #d14;">{A Simple Method for Estimating Evolutionary Rate of Base Substitutions Through Comparative Studies of Nucleotide Sequences}</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="bibtex">  <span class="na" style="color: #008080;">JOURNAL</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Journal of Molecular Evolution}</span><span class="p">,</span></span>

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

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="bibtex">  <span class="na" style="color: #008080;">VOLUME</span> <span class="p">=</span> <span class="s" style="color: #d14;">{16}</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="bibtex">  <span class="na" style="color: #008080;">YEAR</span> <span class="p">=</span> <span class="s" style="color: #d14;">{1980}</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="bibtex">  <span class="na" style="color: #008080;">NUMBER</span> <span class="p">=</span> <span class="s" style="color: #d14;">{2}</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="bibtex">  <span class="na" style="color: #008080;">PAGES</span> <span class="p">=</span> <span class="s" style="color: #d14;">{111-120}</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="bibtex">  <span class="na" style="color: #008080;">DOI</span> <span class="p">=</span> <span class="s" style="color: #d14;">{10.1007/BF01731581}</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="bibtex"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="bibtex"></span></pre>

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<br>

</li>

<li id="d53e5440386e36e96bb1d35d8ad8add7cfdcb87b">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#d53e5440386e36e96bb1d35d8ad8add7cfdcb87b"><strong>libs/pfasta.c</strong></a>

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

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

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

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2015-20<span class="idiff left right">18</span>, Fabian Klötzl <fabian-pfasta@kloetzl.info></span></span>

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<td class="new_line diff-line-num new" 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="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2015-20<span class="idiff left right">20</span>, Fabian Klötzl <fabian-pfasta@kloetzl.info></span></span>

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

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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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4

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Permission to use, copy, modify, and/or distribute this software for any</span></span>

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

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * purpose with or without fee is hereby granted, provided that the above</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,18 +27,24 @@</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>

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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 "pfasta.h"</span></span>

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

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

</pre>

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

30

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

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "v1<span class="idiff left right">4</span>"</span></span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "v1<span class="idiff left right">5</span>"</span></span>

</pre>

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

31

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

31

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

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

</pre>

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

32

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

32

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

<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __SSE2__</span></span>

</pre>

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

33

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

33

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

<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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

35

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

35

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

</pre>

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

36

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

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __STDC_NO_THREADS__</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define thread_local</span></span>

</pre>

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

38

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

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

<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if __STDC_VERSION__ >= 201112L && !defined(__STDC_NO_THREADS__)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <threads.h></span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PFASTA_THREADSAFE 1</span></span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define thread_local</span></span>

</pre>

</td>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PFASTA_THREADSAFE 0</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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

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

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

</pre>

</td>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pfasta_threadsafe</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

</td>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PFASTA_THREADSAFE</span> <span class="p">;</span></span>

</pre>

</td>

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

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

46

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

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

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

47

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

<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"></span>

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

42

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** The following is the maximum length of an error string. It has to be</span></span>

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

43

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * carefully chosen, so that all calls to PF_FAIL_STR succeed. For instance,</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * the line number can account for up to 20 characters.</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +165,8 @@ cleanup:</td>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">buffer_peek</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pfasta_parser</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_ptr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fill_ptr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_ptr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">EOF</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_ptr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fill_ptr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_ptr</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c">                                               <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">EOF</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">buffer_begin</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pfasta_parser</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_ptr</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -257,7 +264,8 @@ size_t count_newlines(const char *begin, const char *end) {</td>

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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">copy_word</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pfasta_parser</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">dynstr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">target</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">return_code</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="old_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">my_isspace</span><span class="p">(</span><span class="n" style="color: #333;">buffer_peek</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">))))</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer_peek</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">),</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">EOF</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">my_isspace</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)))</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC269" 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;">end_of_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_first_space</span><span class="p">(</span><span class="n" style="color: #333;">buffer_begin</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">),</span> <span class="n" style="color: #333;">buffer_end</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">));</span></span>

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

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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">word_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_of_word</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">buffer_begin</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); 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="447" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -439,7 +447,9 @@ int pfasta_read_sequence(struct pfasta_parser *pp, struct pfasta_record *pr) {</td>

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439

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<td class="new_line diff-line-num" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c">            <span class="n" style="color: #333;">PF_FAIL_STR</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="s" style="color: #d14;">"Empty sequence on line %zu."</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">line_number</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="c">    <span class="n" style="color: #333;">PF_FAIL_BUBBLE_CHECK</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">check</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">isalpha</span><span class="p">(</span><span class="n" style="color: #333;">buffer_peek</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">))))</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Assume a line begins only with alpha, -, *, or more spaces</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer_peek</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">),</span> <span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">isalpha</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</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;">c</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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy_word</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UNLIKELY</span><span class="p">(</span><span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">E_EOF</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c">            <span class="n" style="color: #333;">PF_FAIL_BUBBLE_CHECK</span><span class="p">(</span><span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">check</span><span class="p">);</span></span>

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<br>

</li>

<li id="3aab6304ca2cf0f34ba9680d12c87d6b0e5cfead">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#3aab6304ca2cf0f34ba9680d12c87d6b0e5cfead"><strong>libs/pfasta.h</strong></a>

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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2015-20<span class="idiff left right">18</span>, Fabian Klötzl <fabian-pfasta@kloetzl.info></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2015-20<span class="idiff left right">20</span>, Fabian Klötzl <fabian-pfasta@kloetzl.info></span></span>

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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;"> * Permission to use, copy, modify, and/or distribute this software for any</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * purpose with or without fee is hereby granted, provided that the above</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,11 +83,10 @@ void pfasta_free(struct pfasta_parser *pp);</td>

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<pre style="margin: 0;"> <span id="LC83" 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="LC84" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pfasta_version</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __STDC_NO_THREADS__</span></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** If the preprocessor macro `PFASTA_NO_THREADS` is defined, the parser is not</span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * fully thread safe. */</span></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PFASTA_NO_THREADS</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC86" 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="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Returns 0 iff pfasta is not threadsafe.</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pfasta_threadsafe</span><span class="p">();</span></span>

</pre>

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91

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>

</pre>

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

</pre>

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<br>

</li>

<li id="28db630a02e8ffab6561cceefc6c8e0426b5e1b0">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#28db630a02e8ffab6561cceefc6c8e0426b5e1b0"><strong>scripts/_andi</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,6 +25,7 @@ args+=(</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">             Raw\:Uncorrected\ distances</span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">             JC\:Jukes\-Cantor\ corrected</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">             Kimura\:Kimura\-two\-parameter</span>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">             LogDet\:Logarithmic\ determinant</span>

</pre>

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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">     "($info)-p+[Significance of an anchor; default\: 0.025]:float:"</span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">     "($info)--progress=[Show progress bar]:when:(always auto never)"</span>

</pre>

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<br>

</li>

<li id="67e794015a01b8816bd16290e5f8538236da8245">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</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">@@ -4,7 +4,7 @@ andi_SOURCES = andi.c esa.c process.c sequence.c io.c global.h esa.h process.h s</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make">model.h model.c</span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">andi_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/libs <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/opt <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">andi_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-Wno-missing-field-initializers</span></span>

</pre>

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

7

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">andi_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left">$(PSUFSORT)</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(top_builddir)</span>/libs/libpfasta.a <span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">andi_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(top_builddir)</span>/libs/libpfasta.a <span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

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8

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">perf</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nl">perf</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CFLAGS+= -g -O3 -ggdb -fno-omit-frame-pointer</span></span>

</pre>

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<br>

</li>

<li id="e4121eb35479a00bb2becf6c512563545bb34482">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#e4121eb35479a00bb2becf6c512563545bb34482"><strong>src/andi.c</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +142,7 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"></span>

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

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c">                                    <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span><span class="s" style="color: #d14;">"A probability should be a value between 0 and "</span></span>

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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c">                                                      <span class="s" style="color: #d14;">"1, exlusive; Ignoring -p %f argument."</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">                                                      <span class="s" style="color: #d14;">"1, ex<span class="idiff left right">c</span>lusive; Ignoring -p %f argument."</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c">                                                      <span class="n" style="color: #333;">prop</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">                            <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,17 +199,17 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">:</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c">                            <span class="c1" style="color: #998; font-style: italic;">// valid options are 'RAW' and 'JC'</span></span>

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<td class="old_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"RAW"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c">                                    <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_RAW</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"JC"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">                                    <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_JC</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"KIMURA"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c">                                    <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_KIMURA</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"LOGDET"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c">                                    <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_LOGDET</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC210" 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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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c">                                    <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Ignoring argument for --model. Expected Raw, JC or "</span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Kimura"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c">                                    <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span><span class="s" style="color: #d14;">"Ignoring argument for --model. Expected Raw, "</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c">                                                      <span class="s" style="color: #d14;">"JC, Kimura or LogDet"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -340,14 +340,13 @@ void usage(int status) {</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c">            <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Use '-' as file name to read from stdin.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c">            <span class="s" style="color: #d14;">"Options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c">            <span class="s" style="color: #d14;">"  -b, --bootstrap=INT  Print additional bootstrap matrices</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c">            <span class="s" style="color: #d14;">"      --file-of-filenames=FILE  Read additional filenames from "</span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c">            <span class="s" style="color: #d14;">"<span class="idiff left right">FILE; </span>one per line</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c">            <span class="s" style="color: #d14;">"      --file-of-filenames=FILE  Read additional filenames from <span class="idiff left right">FILE; </span>"</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c">            <span class="s" style="color: #d14;">"one per line</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c">            <span class="s" style="color: #d14;">"  -j, --join           Treat all sequences from one file as a single "</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c">            <span class="s" style="color: #d14;">"genome</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c">            <span class="s" style="color: #d14;">"  -l, --low-memory     Use less memory at the cost of speed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c">            <span class="s" style="color: #d14;">"  -m, --model=MODEL    Pick an evolutionary model of 'Raw', 'JC', "</span></span>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c">            <span class="s" style="color: #d14;">"'Kimura'; default: "</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c">            <span class="s" style="color: #d14;">"JC</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c">            <span class="s" style="color: #d14;">"'Kimura', 'LogDet'; default: JC</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c">            <span class="s" style="color: #d14;">"  -p FLOAT             Significance of an anchor; default: 0.025</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="c">            <span class="s" style="color: #d14;">"      --progress=WHEN  Print a progress bar 'always', 'never', or "</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c">            <span class="s" style="color: #d14;">"'auto'; default: auto</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<br>

</li>

<li id="c30c220576b993ebc2341d565eb0ff0c4a10da82">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#c30c220576b993ebc2341d565eb0ff0c4a10da82"><strong>src/global.h</strong></a>

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

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<pre style="margin: 0;"> <span id="LC47" 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="LC48" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MODEL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">M_RAW</span><span class="p">,</span> <span class="n" style="color: #333;">M_JC</span><span class="p">,</span> <span class="n" style="color: #333;">M_KIMURA</span> <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">M_RAW</span><span class="p">,</span> <span class="n" style="color: #333;">M_JC</span><span class="p">,</span> <span class="n" style="color: #333;">M_KIMURA</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LOGDET</span></span> <span class="p">};</span></span>

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

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<pre style="margin: 0;"> <span id="LC52" 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="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This enum contains the available flags. Please note that all</span></span>

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<br>

</li>

<li id="0f3044ba93433ecc1c927c85984cb8dc55b76b9f">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#0f3044ba93433ecc1c927c85984cb8dc55b76b9f"><strong>src/io.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">@@ -227,7 +227,6 @@ void read_fasta(const char *file_name, dsa_t *dsa) {</td>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c">            <span class="n" style="color: #333;">pfasta_record_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pr</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c">    <span class="p">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"><span class="nl">fail:</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c">    <span class="n" style="color: #333;">pfasta_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pp</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c">    <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">file_descriptor</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -264,6 +263,7 @@ void print_distances(const struct model *D, const seq_t *sequences, size_t n,</td>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * compiler warnings. The real default is set in andi.c.*/</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c">            <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_JC</span><span class="p">:</span> <span class="n" style="color: #333;">estimate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">estimate_JC</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c">            <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_KIMURA</span><span class="p">:</span> <span class="n" style="color: #333;">estimate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">estimate_KIMURA</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">            <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_LOGDET</span><span class="p">:</span> <span class="n" style="color: #333;">estimate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">estimate_LOGDET</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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</li>

<li id="93f5f7039d98b42c276a3759cba8ff5bea5a2d7e">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#93f5f7039d98b42c276a3759cba8ff5bea5a2d7e"><strong>src/model.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">@@ -80,7 +80,8 @@ double model_coverage(const model *MM) {</td>

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<pre style="margin: 0;"> <span id="LC80" 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="LC81" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_RAW</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MM</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_total</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">SNPs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">,</span> <span class="n" style="color: #333;">GtoT</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">SNPs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span> <span class="n" style="color: #333;">CtoA</span><span class="p">,</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">,</span> <span class="n" style="color: #333;">GtoA</span><span class="p">,</span> <span class="n" style="color: #333;">GtoC</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c">                                                     <span class="n" style="color: #333;">GtoT</span><span class="p">,</span> <span class="n" style="color: #333;">TtoA</span><span class="p">,</span> <span class="n" style="color: #333;">TtoC</span><span class="p">,</span> <span class="n" style="color: #333;">TtoG</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// Insignificant results. All abort the fail train.</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,8 +112,9 @@ double estimate_JC(const model *MM) {</td>

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<pre style="margin: 0;"> <span id="LC112" 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="LC113" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_KIMURA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MM</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_total</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">transitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">transversions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span> <span class="n" style="color: #333;">GtoC</span><span class="p">,</span> <span class="n" style="color: #333;">GtoT</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">transitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">GtoA</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">,</span> <span class="n" style="color: #333;">TtoC</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">transversions</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c">            <span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">CtoA</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span> <span class="n" style="color: #333;">TtoA</span><span class="p">,</span> <span class="n" style="color: #333;">GtoC</span><span class="p">,</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span> <span class="n" style="color: #333;">GtoT</span><span class="p">,</span> <span class="n" style="color: #333;">TtoG</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">transitions</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">nucl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">transversions</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">nucl</span><span class="p">;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -124,6 +126,77 @@ double estimate_KIMURA(const model *MM) {</td>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">dist</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** @brief computes the evolutionary distance using LogDet.</span></span>

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<pre style="margin: 0;">+<span id="LC130" 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="LC131" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The LogDet distance between sequence X and and sequence Y</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * is given as</span></span>

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<pre style="margin: 0;">+<span id="LC133" 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="LC134" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * -(1 / K) * (log(det(Fxy)) - 0.5 * log(det(Fxx * Fyy)))</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Where K is the number of character states, Fxy is the site-pattern</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * frequency matrix, and diagonal matrices Fxx and Fyy give the</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * frequencies of the different character states in sequences X and Y.</span></span>

</pre>

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

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Each i,j-th entry in Fxy is the proportion of homologous sites</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * where sequences X and Y have character states i and j, respectively.</span></span>

</pre>

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

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For our purposes, X is the Subject (From) sequence and Y is the</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Query (To) sequence and matrix Fxy looks like</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  To   A  C  G  T</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * From</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  A  (            )</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  C  (            )</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  G  (            )</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  T  (            )</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param MM - The mutation matrix.</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns The LogDet distance.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_LOGDET</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MM</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

158

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">model_total</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">logDetFxxFyy</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// log determinant of diagonal matrix of row sums</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoA</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">CtoA</span><span class="p">,</span> <span class="n" style="color: #333;">CtoC</span><span class="p">,</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">GtoA</span><span class="p">,</span> <span class="n" style="color: #333;">GtoC</span><span class="p">,</span> <span class="n" style="color: #333;">GtoG</span><span class="p">,</span> <span class="n" style="color: #333;">GtoT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">TtoA</span><span class="p">,</span> <span class="n" style="color: #333;">TtoC</span><span class="p">,</span> <span class="n" style="color: #333;">TtoG</span><span class="p">,</span> <span class="n" style="color: #333;">TtoT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// log determinant of diagonal matrix of column sums</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoA</span><span class="p">,</span> <span class="n" style="color: #333;">CtoA</span><span class="p">,</span> <span class="n" style="color: #333;">GtoA</span><span class="p">,</span> <span class="n" style="color: #333;">TtoA</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span> <span class="n" style="color: #333;">CtoC</span><span class="p">,</span> <span class="n" style="color: #333;">GtoC</span><span class="p">,</span> <span class="n" style="color: #333;">TtoC</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span> <span class="n" style="color: #333;">GtoG</span><span class="p">,</span> <span class="n" style="color: #333;">TtoG</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c">            <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">model_sum</span><span class="p">(</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span> <span class="n" style="color: #333;">CtoT</span><span class="p">,</span> <span class="n" style="color: #333;">GtoT</span><span class="p">,</span> <span class="n" style="color: #333;">TtoT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nucl</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// determinant of the site-pattern frequency matrix</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">detFxy</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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

</pre>

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

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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</td>

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

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoT</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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

<pre style="margin: 0;">+<span id="LC191" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoG</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

192

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

<pre style="margin: 0;">+<span id="LC192" class="line" lang="c">            <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">AtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">CtoG</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoC</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">TtoA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">P</span><span class="p">[</span><span class="n" style="color: #333;">GtoC</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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

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

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">detFxy</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">logDetFxxFyy</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// fix negative zero</span></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">dist</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** @brief Bootstrap a mutation matrix.</span></span>

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<pre style="margin: 0;"> <span id="LC201" 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="LC202" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The classical bootstrapping process, as described by Felsenstein, resamples</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,25 +205,17 @@ double estimate_KIMURA(const model *MM) {</td>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * resample the elements of the mutation matrix. See Klötzl & Haubold (2016)</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * for details. http://www.mdpi.com/2075-1729/6/1/11/htm</span></span>

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<pre style="margin: 0;"> <span id="LC207" 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="LC135" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param <span class="idiff left right">MM</span> - The original mutation matrix.</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param <span class="idiff left right">datum</span> - The original mutation matrix.</span></span>

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns A bootstrapped mutation matrix.</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"><span class="n" style="color: #333;">model</span> <span class="nf" style="color: #900; font-weight: 600;">model_bootstrap</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="n" style="color: #333;">MM</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c">    <span class="n" style="color: #333;">model</span> <span class="n" style="color: #333;">datum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_total</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

211

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"><span class="n" style="color: #333;">model</span> <span class="nf" style="color: #900; font-weight: 600;">model_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">model</span> <span class="n" style="color: #333;">datum</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

212

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nucl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_total</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">datum</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

213

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">];</span></span>

</pre>

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

143

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

214

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c">            <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">MM</span></span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">nucl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

215

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c">            <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">datum</span></span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">nucl</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

145

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

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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

217

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

<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

147

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

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

<pre style="margin: 0;">-<span id="LC147" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

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

<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

149

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

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

<pre style="margin: 0;">-<span id="LC149" class="line" lang="c">    <span class="n" style="color: #333;">gsl_ran_multinomial</span><span class="p">(</span><span class="n" style="color: #333;">RNG</span><span class="p">,</span> <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">,</span> <span class="n" style="color: #333;">nucl</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

150

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

</td>

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

<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

151

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

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

<pre style="margin: 0;">-<span id="LC151" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC152" class="line" lang="c">            <span class="n" style="color: #333;">datum</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC153" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c">    <span class="n" style="color: #333;">gsl_ran_multinomial</span><span class="p">(</span><span class="n" style="color: #333;">RNG</span><span class="p">,</span> <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">,</span> <span class="n" style="color: #333;">nucl</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">datum</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">datum</span><span class="p">;</span></span>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,7 +281,7 @@ void model_count_equal(model *MM, const char *S, size_t len) {</td>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param c - input nucleotide</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns 2bit representation.</span></span>

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<pre style="margin: 0;"> <span id="LC283" 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="LC219" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="nf" style="color: #900; font-weight: 600;">nucl2bit</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="nf" style="color: #900; font-weight: 600;">nucl2bit</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c">    <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">&=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c">    <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,25 +309,13 @@ void model_count(model *MM, const char *S, const char *Q, size_t len) {</td>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// Pick the correct two bits representing s and q.</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucl2bit</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">baz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucl2bit</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC249" 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="LC250" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * The mutation matrix is symmetric. For convenience we define the</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * mutation XtoY with X > Y.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" 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="LC253" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">baz</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">foo</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">foo</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c">                    <span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baz</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c">                    <span class="n" style="color: #333;">baz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c">            <span class="p">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">bar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucl2bit</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC314" 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="LC315" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * Finally, we want to map the indices to the correct mutation. This is</span></span>

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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * done by utilising the mutation types in model.h.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 */</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c">            <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">map4</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x9740</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">map4</span> <span class="o" style="font-weight: 600;">>></span> <span class="p">(</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">baz</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xf</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">baz</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c">            <span class="n" style="color: #333;">local_counts</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c">    <span class="p">}</span></span>

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</li>

<li id="91f1a287183fa08d7cffd01580a5050be8989762">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#91f1a287183fa08d7cffd01580a5050be8989762"><strong>src/model.h</strong></a>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This enum contains all possible mutations. Some of them are considered</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * symmetric (e.g. AtoT and TtoA) and thus have the same value. The total number</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This enum contains all possible mutations. The total number</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * of different possible mutations is MUTCOUNTS.</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="old_line diff-line-num" 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="LC14" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span></span>

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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>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,19 +16,19 @@ enum {</td>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c">     <span class="n" style="color: #333;">AtoC</span><span class="p">,</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">     <span class="n" style="color: #333;">AtoG</span><span class="p">,</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     <span class="n" style="color: #333;">AtoT</span><span class="p">,</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c">     <span class="n" style="color: #333;">CtoA</span><span class="p">,</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c">     <span class="n" style="color: #333;">CtoC</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

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

<pre style="margin: 0;"> <span id="LC21" class="line" lang="c">     <span class="n" style="color: #333;">CtoG</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

22

</td>

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

22

</td>

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">     <span class="n" style="color: #333;">CtoT</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

</td>

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="c">     <span class="n" style="color: #333;">GtoA</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

</td>

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="n" style="color: #333;">GtoC</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

23

</td>

<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

</td>

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     <span class="n" style="color: #333;">GtoG</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

24

</td>

<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

</td>

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

<pre style="margin: 0;"> <span id="LC26" class="line" lang="c">     <span class="n" style="color: #333;">GtoT</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

27

</td>

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">     <span class="n" style="color: #333;">TtoA</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="c">     <span class="n" style="color: #333;">TtoC</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="c">     <span class="n" style="color: #333;">TtoG</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

</td>

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

30

</td>

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">     <span class="n" style="color: #333;">TtoT</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

26

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="c">     <span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

27

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="c">     <span class="n" style="color: #333;">CtoA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtoC</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

28

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC28" class="line" lang="c">     <span class="n" style="color: #333;">GtoA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtoG</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

29

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="c">     <span class="n" style="color: #333;">GtoC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CtoG</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

30

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="c">     <span class="n" style="color: #333;">TtoA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtoT</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

31

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="c">     <span class="n" style="color: #333;">TtoC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CtoT</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

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

32

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="c">     <span class="n" style="color: #333;">TtoG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GtoT</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

31

</td>

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="c">     <span class="n" style="color: #333;">MUTCOUNTS</span></span>

</pre>

</td>

</tr>

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

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

33

</td>

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

32

</td>

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

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

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

</td>

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

33

</td>

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

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

</pre>

</td>

</tr>

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

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

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** @brief The mutation matrix.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,12 +45,15 @@ enum {</td>

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<pre style="margin: 0;"> <span id="LC45" 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="LC46" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The cells are absolute counts. Together with seq_len (the query length),</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * we can deduce the substitution rate and coverage.</span></span>

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<pre style="margin: 0;">+<span id="LC48" 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="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * As libdivsufsort is 32 bit the sequence length is limited to (INT_MAX-1)/2.</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * We can thus use the same limit for the counts.</span></span>

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<pre style="margin: 0;"> <span id="LC51" 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="LC52" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">model</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c">     <span class="cm" style="color: #998; font-style: italic;">/** The absolute counts of mutation types. */</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">in</span>t</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c">     <span class="cm" style="color: #998; font-style: italic;">/** The query length. */</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">seq_len</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">in</span>t</span> <span class="n" style="color: #333;">seq_len</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">model</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">model_count_equal</span><span class="p">(</span><span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">);</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,4 +63,5 @@ double model_coverage(const model *);</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_RAW</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_JC</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_KIMURA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="c"><span class="n" style="color: #333;">model</span> <span class="nf" style="color: #900; font-weight: 600;">model_bootstrap</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span><span class="p">);</span></span></pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_LOGDET</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="n" style="color: #333;">model</span> <span class="nf" style="color: #900; font-weight: 600;">model_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">);</span></span></pre>

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<br>

</li>

<li id="01a89d148d2434a88bba979e1ef4be45506178a5">

<a href="https://salsa.debian.org/med-team/andi/-/commit/70820b092e7429fa2ac3c4a3e4175dca7eab272c#01a89d148d2434a88bba979e1ef4be45506178a5"><strong>test/Makefile.am</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,12 +9,12 @@ test_seq_LDADD = $(GLIB_LIBS) $(top_builddir)/opt/libcompat.a</td>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">test_process_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_process.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/esa.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/io.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/model.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/process.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/sequence.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/global.h</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">test_process_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/src <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/opt <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/libs <span class="nt" style="color: #000080;">-DDEBUG</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">test_process_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nv" style="color: #008080;">$(GLIB_CFLAGS)</span> <span class="nt" style="color: #000080;">-Wno-missing-field-initializers</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">test_process_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(GLIB_LIBS)</span> <span class="nv" style="color: #008080;"><span class="idiff left">$(PSUFSORT)</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a <span class="nv" style="color: #008080;">$(top_builddir)</span>/libs/libpfasta.a</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">test_process_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(GLIB_LIBS)</span> <span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a <span class="nv" style="color: #008080;">$(top_builddir)</span>/libs/libpfasta.a</span>

</pre>

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">test_esa_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_esa.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/esa.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/sequence.c <span class="nv" style="color: #008080;">$(top_srcdir)</span>/src/esa.h</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="make"><span class="nv" style="color: #008080;">test_esa_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/libs <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/opt <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(top_srcdir)</span>/src <span class="nt" style="color: #000080;">-DDEBUG</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">test_esa_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nv" style="color: #008080;">$(GLIB_CFLAGS)</span> <span class="nt" style="color: #000080;">-Wno-missing-field-initializers</span></span>

</pre>

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

17

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

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">test_esa_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(GLIB_LIBS)</span> <span class="nv" style="color: #008080;"><span class="idiff left">$(PSUFSORT)</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">test_esa_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(GLIB_LIBS)</span> <span class="nv" style="color: #008080;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

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

18

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

18

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

</pre>

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

19

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

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nv" style="color: #008080;">test_fasta_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_fasta.cxx</span>

</pre>

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

20

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

20

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

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

</pre>

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