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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/snp-sites">Debian Med / snp-sites</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12">b4b20798</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-10-23T16:45:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.1</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
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<li class="file-stats">
<a href="#dad57a4c245a8007c90257aef0514c8b6a0f600c">
AUTHORS
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<span class="new-file">
+
CHANGELOG.md
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</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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</li>
<li class="file-stats">
<a href="#4da47274165db9da0ac4655328b16d9b7b371311">
src/alignment-file.c
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</li>
<li class="file-stats">
<a href="#ff3ebe958bac770ac9c7e5c041ec27988b87195a">
src/alignment-file.h
</a>
</li>
<li class="file-stats">
<a href="#3a576e09615c0e19842e5f3ac31e858c9ae7fe41">
src/main.c
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<li class="file-stats">
<a href="#4404f3ee90418384e32d187e31058405ada49f7f">
src/snp-sites.c
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<li class="file-stats">
<a href="#db1dd37478974d6c152c3417ce7729ef538e9921">
src/snp-sites.h
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<li class="file-stats">
<a href="#0d1a811dfea95ad0b68315ebf50f3c0dfbd49a3d">
tests/check-snp-sites.c
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</li>
<li class="file-stats">
<a href="#dd9a28dafeb8d6903112bc48ebac2897525e3787">
<span class="new-file">
+
tests/data/small_alignment.constant_site_counts.txt
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</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -2,7 +2,13 @@ language: c</td>
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<td class="diff-line-num 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">
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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>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<td class="diff-line-num 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">check</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -qq check</span> </span>
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">autoreconf -i && ./configure && make && make check</span></span></pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">autoreconf -i && ./configure --enable-maintainer-mode CFLAGS='-O0 --coverage' && make && make check</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash <(curl -s https://codecov.io/bash)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#dad57a4c245a8007c90257aef0514c8b6a0f600c"><strong>AUTHORS</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Andrew J. Page <ap13@sanger.ac.uk></span>
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2
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<td class="diff-line-num 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">
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="plaintext">Ben Taylor <path-help@sanger.ac.uk></span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Jorge Soares <path-help@sanger.ac.uk></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Peter van Heusden</span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change Log</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Unreleased](https://github.com/sanger-pathogens/snp-sites/tree/HEAD)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/v2.4.1...HEAD</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> SegFault for unknown reason <span class="p">[</span><span class="nv" style="color: #008080;">\#72</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/72</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">-</span> Include tests in README <span class="p">[</span><span class="nv" style="color: #008080;">\#73</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/73</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.4.1](https://github.com/sanger-pathogens/snp-sites/tree/v2.4.1) (2018-10-04)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/v2.4.0...v2.4.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Implemented enhancements:**</span></span>
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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="p">-</span> Print to screen <span class="p">[</span><span class="nv" style="color: #008080;">\#63</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/63</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">-</span> Docker file typo <span class="p">[</span><span class="nv" style="color: #008080;">\#60</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/60</span><span class="p">)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">-</span> Info in VCF output format <span class="p">[</span><span class="nv" style="color: #008080;">\#68</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/68</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">-</span> Include docker and conda badges <span class="p">[</span><span class="nv" style="color: #008080;">\#70</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/70</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">-</span> fixed Dockerfile <span class="p">[</span><span class="nv" style="color: #008080;">\#67</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/67</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[trstickland](https://github.com/trstickland</span><span class="p">)</span>)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.4.0](https://github.com/sanger-pathogens/snp-sites/tree/v2.4.0) (2018-01-29)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.3.3...v2.4.0</span><span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p">-</span> segmentation fault with <span class="sb" style="color: #d14;">`-b`</span> option <span class="p">[</span><span class="nv" style="color: #008080;">\#58</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/58</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">-</span> Segmentation fault with larger sequences <span class="se" style="color: #d14;">\(</span>on Desktop and HPC<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: #008080;">\#57</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/57</span><span class="p">)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">-</span> Gaps not reported in output? <span class="p">[</span><span class="nv" style="color: #008080;">\#61</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/61</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">-</span> update readme <span class="p">[</span><span class="nv" style="color: #008080;">\#65</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/65</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p">-</span> Jk seg fault <span class="p">[</span><span class="nv" style="color: #008080;">\#59</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/59</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.3.3](https://github.com/sanger-pathogens/snp-sites/tree/2.3.3) (2017-06-09)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.3.2...2.3.3</span><span class="p">)</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">-</span> brew recipe needs to be updated to the latest release. <span class="p">[</span><span class="nv" style="color: #008080;">\#55</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/55</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="p">-</span> Linuxbrew installation issue <span class="se" style="color: #d14;">\(</span>links issue<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: #008080;">\#54</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/54</span><span class="p">)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">-</span> update LICENSE and AUTHORS <span class="p">[</span><span class="nv" style="color: #008080;">\#56</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/56</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.3.2](https://github.com/sanger-pathogens/snp-sites/tree/2.3.2) (2016-05-12)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.3.1...2.3.2</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">-</span> Didn't mean to open this <span class="p">[</span><span class="nv" style="color: #008080;">\#52</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/52</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="p">-</span> Failing tests on various platforms <span class="p">[</span><span class="nv" style="color: #008080;">\#51</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/51</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.3.1](https://github.com/sanger-pathogens/snp-sites/tree/2.3.1) (2016-03-18)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.3.0...2.3.1</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="p">-</span> allow pure bases and monomorphic, making it work with BEAST <span class="p">[</span><span class="nv" style="color: #008080;">\#50</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/50</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.3.0](https://github.com/sanger-pathogens/snp-sites/tree/2.3.0) (2016-03-17)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.2.2...2.3.0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.2.2](https://github.com/sanger-pathogens/snp-sites/tree/2.2.2) (2016-03-14)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.2.1...2.2.2</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">-</span> make sure original API is not changed <span class="p">[</span><span class="nv" style="color: #008080;">\#49</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/49</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="p">-</span> update to 2.2.1 <span class="p">[</span><span class="nv" style="color: #008080;">\#48</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/48</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.2.1](https://github.com/sanger-pathogens/snp-sites/tree/2.2.1) (2016-03-11)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.2.0...2.2.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="p">-</span> adjust manpage <span class="p">[</span><span class="nv" style="color: #008080;">\#47</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/47</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="p">-</span> output reference and change name to snp-sites <span class="p">[</span><span class="nv" style="color: #008080;">\#46</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/46</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.2.0](https://github.com/sanger-pathogens/snp-sites/tree/2.2.0) (2016-03-11)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.1.3...2.2.0</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="p">-</span> Build is failing on Mac OS <span class="p">[</span><span class="nv" style="color: #008080;">\#45</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/45</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="p">-</span> specify reference sequence <span class="p">[</span><span class="nv" style="color: #008080;">\#44</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/44</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">-</span> Add Arxiv paper link to README.md <span class="p">[</span><span class="nv" style="color: #008080;">\#43</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/43</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.1.3](https://github.com/sanger-pathogens/snp-sites/tree/2.1.3) (2016-01-27)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.1.1...2.1.3</span><span class="p">)</span></span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="p">-</span> possible to convert to redhat? <span class="p">[</span><span class="nv" style="color: #008080;">\#39</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/39</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="p">-</span> Ensure C99 compliance <span class="p">[</span><span class="nv" style="color: #008080;">\#42</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/42</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[AidanDelaney](https://github.com/AidanDelaney</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="p">-</span> Test data <span class="p">[</span><span class="nv" style="color: #008080;">\#41</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/41</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="p">-</span> Running the clang static analyser turns up an issue with unintialised… <span class="p">[</span><span class="nv" style="color: #008080;">\#40</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/40</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[AidanDelaney](https://github.com/AidanDelaney</span><span class="p">)</span>)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.1.1](https://github.com/sanger-pathogens/snp-sites/tree/2.1.1) (2015-12-14)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.1.0...2.1.1</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Implemented enhancements:**</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="p">-</span> Opens <span class="se" style="color: #d14;">\<</span>file<span class="se" style="color: #d14;">\></span> twice? <span class="p">[</span><span class="nv" style="color: #008080;">\#26</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/26</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"><span class="p">-</span> make check =<span class="se" style="color: #d14;">\></span> cannot find -lsubunit <span class="p">[</span><span class="nv" style="color: #008080;">\#33</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/33</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">-</span> autoreconf -i warnings =<span class="se" style="color: #d14;">\></span> option 'subdir-objects' is disabled <span class="p">[</span><span class="nv" style="color: #008080;">\#29</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/29</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p">-</span> Autotoolize checking for dependencies <span class="p">[</span><span class="nv" style="color: #008080;">\#38</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/38</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.1.0](https://github.com/sanger-pathogens/snp-sites/tree/2.1.0) (2015-12-03)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.0.3...2.1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"><span class="p">-</span> Reduce times input file is opened <span class="p">[</span><span class="nv" style="color: #008080;">\#37</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/37</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.0.3](https://github.com/sanger-pathogens/snp-sites/tree/2.0.3) (2015-12-03)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.0.2...2.0.3</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="p">-</span> How do we run the tests? <span class="p">[</span><span class="nv" style="color: #008080;">\#30</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/30</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"><span class="p">-</span> Add a --version switch? <span class="p">[</span><span class="nv" style="color: #008080;">\#27</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/27</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="p">-</span> FYI - updated brew package to 2.x series <span class="p">[</span><span class="nv" style="color: #008080;">\#24</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues/24</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="p">-</span> Bump version to 2.0.3 <span class="p">[</span><span class="nv" style="color: #008080;">\#36</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/36</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"><span class="p">-</span> 496468: Allow '?' in fasta input <span class="p">[</span><span class="nv" style="color: #008080;">\#35</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/35</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"><span class="p">-</span> Major cleanup to use standard C string functions <span class="p">[</span><span class="nv" style="color: #008080;">\#34</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/34</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[tseemann](https://github.com/tseemann</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="p">-</span> Add -V version flag <span class="se" style="color: #d14;">\(</span>Issue <span class="se" style="color: #d14;">\#</span>27<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: #008080;">\#32</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/32</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[tseemann](https://github.com/tseemann</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="p">-</span> Use stdio FILENAME<span class="se" style="color: #d14;">\_</span>MAX for path char<span class="se" style="color: #d14;">\[\]</span> sizes <span class="p">[</span><span class="nv" style="color: #008080;">\#31</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/31</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[tseemann](https://github.com/tseemann</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"><span class="p">-</span> fix recent compilation failure in Debian <span class="p">[</span><span class="nv" style="color: #008080;">\#23</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/23</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[satta](https://github.com/satta</span><span class="p">)</span>)</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.0.2](https://github.com/sanger-pathogens/snp-sites/tree/2.0.2) (2015-09-03)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/2.0.1...2.0.2</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p">-</span> Remove a tab in VCF header <span class="p">[</span><span class="nv" style="color: #008080;">\#22</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/22</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"><span class="p">-</span> Added bt5 and Jorge emails <span class="se" style="color: #d14;">\(</span>Jorge as path-help<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: #008080;">\#21</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/21</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aslett1](https://github.com/aslett1</span><span class="p">)</span>)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.0.1](https://github.com/sanger-pathogens/snp-sites/tree/2.0.1) (2015-07-17)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.5.0...2.0.1</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="p">-</span> Add reference sequence length to VCF output <span class="p">[</span><span class="nv" style="color: #008080;">\#20</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/20</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"><span class="p">-</span> Change output format to show Genotype rather than Alt Base <span class="p">[</span><span class="nv" style="color: #008080;">\#19</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/19</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="p">-</span> Reformat README <span class="p">[</span><span class="nv" style="color: #008080;">\#18</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/18</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.5.0](https://github.com/sanger-pathogens/snp-sites/tree/1.5.0) (2014-02-01)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.11...1.5.0</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.11](https://github.com/sanger-pathogens/snp-sites/tree/1.4.11) (2014-01-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.10...1.4.11</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.10](https://github.com/sanger-pathogens/snp-sites/tree/1.4.10) (2014-01-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.9...1.4.10</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.9](https://github.com/sanger-pathogens/snp-sites/tree/1.4.9) (2014-01-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.8...1.4.9</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.8](https://github.com/sanger-pathogens/snp-sites/tree/1.4.8) (2014-01-23)</span></span>
</pre>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.7...1.4.8</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.7](https://github.com/sanger-pathogens/snp-sites/tree/1.4.7) (2014-01-23)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.6...1.4.7</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.6](https://github.com/sanger-pathogens/snp-sites/tree/1.4.6) (2014-01-23)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.5...1.4.6</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.5](https://github.com/sanger-pathogens/snp-sites/tree/1.4.5) (2014-01-23)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.4...1.4.5</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.4](https://github.com/sanger-pathogens/snp-sites/tree/1.4.4) (2014-01-23)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.3...1.4.4</span><span class="p">)</span></span>
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204
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.3](https://github.com/sanger-pathogens/snp-sites/tree/1.4.3) (2014-01-23)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.2...1.4.3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.2](https://github.com/sanger-pathogens/snp-sites/tree/1.4.2) (2014-01-23)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4.1...1.4.2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4.1](https://github.com/sanger-pathogens/snp-sites/tree/1.4.1) (2014-01-21)</span></span>
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<td class="diff-line-num new new_line" 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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.4...1.4.1</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.4](https://github.com/sanger-pathogens/snp-sites/tree/1.4) (2014-01-20)</span></span>
</pre>
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<td class="diff-line-num new new_line" 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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.3...1.4</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3](https://github.com/sanger-pathogens/snp-sites/tree/1.3) (2014-01-15)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.2...1.3</span><span class="p">)</span></span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2](https://github.com/sanger-pathogens/snp-sites/tree/1.2) (2014-01-14)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.1...1.2</span><span class="p">)</span></span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.1](https://github.com/sanger-pathogens/snp-sites/tree/1.1) (2014-01-13)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/1.0...1.1</span><span class="p">)</span></span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.0](https://github.com/sanger-pathogens/snp-sites/tree/1.0) (2014-01-06)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/compare/0.1...1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1](https://github.com/sanger-pathogens/snp-sites/tree/0.1) (2013-07-25)</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="p">-</span> travis install check <span class="p">[</span><span class="nv" style="color: #008080;">\#17</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/17</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"><span class="p">-</span> travis autoreconf <span class="p">[</span><span class="nv" style="color: #008080;">\#16</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/16</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="p">-</span> travis ci <span class="p">[</span><span class="nv" style="color: #008080;">\#15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/15</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="p">-</span> Update version and readme <span class="p">[</span><span class="nv" style="color: #008080;">\#14</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/14</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="p">-</span> Fix memory leaks <span class="p">[</span><span class="nv" style="color: #008080;">\#13</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/13</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"><span class="p">-</span> fix memory leaks and update make <span class="p">[</span><span class="nv" style="color: #008080;">\#12</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/12</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="p">-</span> GPL <span class="p">[</span><span class="nv" style="color: #008080;">\#11</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/11</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"><span class="p">-</span> rollback changes to fasta file parsing <span class="p">[</span><span class="nv" style="color: #008080;">\#10</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/10</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="p">-</span> print unequal length error message to stderr <span class="p">[</span><span class="nv" style="color: #008080;">\#9</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/9</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="p">-</span> vcf coords from 1 <span class="p">[</span><span class="nv" style="color: #008080;">\#8</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/8</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"><span class="p">-</span> speedup <span class="p">[</span><span class="nv" style="color: #008080;">\#7</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/7</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="p">-</span> print out an error if the sequence lengths are uneven <span class="p">[</span><span class="nv" style="color: #008080;">\#6</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/6</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="p">-</span> speedup phylip creation <span class="p">[</span><span class="nv" style="color: #008080;">\#5</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/5</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"><span class="p">-</span> output filename <span class="p">[</span><span class="nv" style="color: #008080;">\#4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/4</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"><span class="p">-</span> Tests for when an N is present in input <span class="p">[</span><span class="nv" style="color: #008080;">\#3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/3</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"><span class="p">-</span> Choose output file formats <span class="p">[</span><span class="nv" style="color: #008080;">\#2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/2</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="p">-</span> Treat N as a gap <span class="p">[</span><span class="nv" style="color: #008080;">\#1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/pull/1</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -8,6 +8,7 @@ Rapidly extracts SNPs from a multi-FASTA alignment.</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Container ready</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/container-ready-brightgreen.svg</span><span class="p">)</span>](https://quay.io/repository/biocontainers/gubbins) </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/build/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker Pulls</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/pulls/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![codecov</span><span class="p">](</span><span class="sx" style="color: #d14;">https://codecov.io/gh/sanger-pathogens/snp-sites/branch/master/graph/badge.svg</span><span class="p">)</span>](https://codecov.io/gh/sanger-pathogens/snp-sites) </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +19,7 @@ Rapidly extracts SNPs from a multi-FASTA alignment.</td>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux \- from source</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinux---from-source</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux \- from a release tarball</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinux---from-a-release-tarball</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">All platforms \- Docker</span><span class="p">](</span><span class="sx" style="color: #d14;">#all-platforms---docker</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Running the tests</span><span class="p">](</span><span class="sx" style="color: #d14;">#running-the-tests</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Example input</span><span class="p">](</span><span class="sx" style="color: #d14;">#example-input</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Example usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#example-usage</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -79,6 +81,18 @@ sudo make install</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### All platforms - Docker</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown">Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Running the tests</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown">The test can be run from the top level directory: </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">```</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown">autoreconf -i</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">./configure</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown">make</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">make check</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">This requires libcheck (the <span class="sb" style="color: #d14;">`check`</span> package in Ubuntu) to be installed.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"></span>
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82
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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83
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"></span>
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84
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="p">```</span></span>
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<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.<span class="idiff left right">4</span>.1</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.<span class="idiff left right">5</span>.1</span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ PKG_CHECK_MODULES([CHECK],[check >= 0.8.2],[have_check="yes"],</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> AC_MSG_WARN(["'Check' unit testing framework not found. It would be impossible to run unit tests!"])</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [have_check="no"])</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">AC_CHECK_HEADERS([zlib.h math.h getopt.h])</span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">AC_CHECK_LIB(m, floor)</span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">AX_CHECK_ZLIB</span>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#4da47274165db9da0ac4655328b16d9b7b371311"><strong>src/alignment-file.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">@@ -105,7 +105,11 @@ void get_bases_for_each_snp(char filename[], char ** bases_for_snps)</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_snps</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_snps</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">detect_snps_count_constant_sites</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_snps_count_constant_sites</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"><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;">int</span> <span class="n" style="color: #333;">i</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;">int</span> <span class="n" style="color: #333;">l</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">@@ -113,8 +117,11 @@ void detect_snps(char filename[], int pure_mode, int output_monomorphic)</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">number_of_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">length_of_genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC119" 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;">first_sequence</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* array below allows quick mapping of A, C, T and G characters to indices in base_counts array */</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">char_to_base_count_index</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">};</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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118
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">kseq_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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119
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> </span>
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120
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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,8 +198,12 @@ void detect_snps(char filename[], int pure_mode, int output_monomorphic)</td>
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191
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<td class="diff-line-num new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="p">{</span></span>
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192
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<td class="diff-line-num 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">
199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">snp_locations</span><span class="p">[</span><span class="n" style="color: #333;">current_snp_index</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>
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193
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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">current_snp_index</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="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;">constant_site_counts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_pure</span><span class="p">(</span><span class="n" style="color: #333;">first_sequence</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">[</span><span class="n" style="color: #333;">char_to_base_count_index</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">first_sequence</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>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="p">}</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="p">}</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">first_sequence</span><span class="p">);</span></span>
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197
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">kseq_destroy</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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198
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#ff3ebe958bac770ac9c7e5c041ec27988b87195a"><strong>src/alignment-file.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">@@ -23,6 +23,7 @@</td>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "kseq.h"</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>
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25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_snps</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">);</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">detect_snps_count_constant_sites</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">constant_site_counts</span><span class="p">);</span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">get_bases_for_each_snp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">bases_for_snps</span><span class="p">);</span></span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">is_unknown</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">base</span><span class="p">);</span></span>
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28
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">get_length_of_genome</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#3a576e09615c0e19842e5f3ac31e858c9ae7fe41"><strong>src/main.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">@@ -40,6 +40,7 @@ static void print_usage()</td>
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40
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -p output a phylip file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -o STR specify an output filename [STDOUT]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -c only output columns containing exclusively ACGT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -C only output count of constant sites (suitable for IQ-TREE -fconst) and nothing else</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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43
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -b output monomorphic sites, used for BEAST</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -h this help message</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -V print version and exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,10 +71,11 @@ int main (int argc, char **argv) {</td>
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70
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_vcf_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_phylip_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_constant_site_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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73
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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74
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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75
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> </span>
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76
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<pre style="margin: 0;">-<span id="LC76" 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;">getopt</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"mvrbpco:V"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" 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;">getopt</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"mvrbpc<span class="idiff left right">C</span>o:V"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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77
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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78
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="p">{</span></span>
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79
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81
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<pre style="margin: 0;"> <span id="LC81" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,6 +96,9 @@ int main (int argc, char **argv) {</td>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>
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95
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">pure_mode</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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96
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">:</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">output_constant_site_counts</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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97
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">:</span></span>
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98
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">output_monomorphic</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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99
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -118,8 +123,10 @@ int main (int argc, char **argv) {</td>
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118
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="p">}</span></span>
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119
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> </span>
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120
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">strncpy</span><span class="p">(</span><span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">],</span> <span class="n" style="color: #333;">FILENAME_MAX</span><span class="p">);</span> </span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"> </span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">pure_mode</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">output_constant_site_counts</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">count_constant_sites</span><span class="p">(</span><span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="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;">pure_mode</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span></span>
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123
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="p">{</span></span>
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124
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">generate_snp_sites_with_ref_pure_mono</span><span class="p">(</span><span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">,</span></span>
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125
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<td class="diff-line-num new_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">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">output_multi_fasta_file</span><span class="p">,</span></span>
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<li id="4404f3ee90418384e32d187e31058405ada49f7f">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#4404f3ee90418384e32d187e31058405ada49f7f"><strong>src/snp-sites.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -34,7 +34,8 @@ static int generate_snp_sites_generic(char filename[],</td>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_vcf_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_phylip_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">output_filename</span><span class="p">[],</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_reference</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_reference</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">)</span></span>
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38
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="p">{</span></span>
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39
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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40
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">detect_snps</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,7 +141,32 @@ int generate_snp_sites_with_ref_pure_mono(char filename[],</td>
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140
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">output_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_reference</span><span class="p">,</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">);</span></span>
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141
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="p">}</span></span>
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142
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">count_constant_sites</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">output_filename</span><span class="p">[])</span> <span class="p">{</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">cwd</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">input_file</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">output_file</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">constant_site_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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143
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">output_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">output_file</span><span class="p">)</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"ERROR: cannot open %s for writing: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">,</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">));</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="p">}</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">constant_site_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">constant_site_counts</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"ERROR: cannot allocated memory for constant_site_counts"</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">detect_snps_count_constant_sites</span><span class="p">(</span><span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d,%d,%d,%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">constant_site_counts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">output_file</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">constant_site_counts</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"><span class="p">}</span></span>
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144
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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;">// Inefficient</span></span>
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145
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">strip_directory_from_filename</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_filename</span><span class="p">)</span></span>
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146
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"><span class="p">{</span></span>
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<li id="db1dd37478974d6c152c3417ce7729ef538e9921">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#db1dd37478974d6c152c3417ce7729ef538e9921"><strong>src/snp-sites.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">@@ -22,6 +22,9 @@</td>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _SNP_SITES_H_</span></span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <errno.h></span></span>
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25
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">generate_snp_sites</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[],</span></span>
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27
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_multi_fasta_file</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">@@ -42,7 +45,9 @@ int generate_snp_sites_with_ref_pure_mono(char filename[],</td>
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42
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_reference</span><span class="p">,</span></span>
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43
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pure_mode</span><span class="p">,</span></span>
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44
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">output_monomorphic</span><span class="p">);</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> </span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">count_constant_sites</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">filename</span><span class="p">[]);</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"></span>
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46
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">strip_directory_from_filename</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span></span>
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47
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52
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<pre style="margin: 0;"> <span id="LC52" 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;">output_filename</span><span class="p">);</span></span>
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48
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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<li id="0d1a811dfea95ad0b68315ebf50f3c0dfbd49a3d">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#0d1a811dfea95ad0b68315ebf50f3c0dfbd49a3d"><strong>tests/check-snp-sites.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -269,6 +269,14 @@ START_TEST (check_strip_directory_from_filename_with_directory)</td>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"><span class="p">}</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"><span class="n" style="color: #333;">END_TEST</span></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">START_TEST</span> <span class="p">(</span><span class="n" style="color: #333;">check_count_constant_sites</span><span class="p">)</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c"><span class="p">{</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">count_constant_sites</span><span class="p">(</span><span class="s" style="color: #d14;">"../tests/data/small_alignment.aln"</span><span class="p">,</span> <span class="s" style="color: #d14;">"small_alignment.constant_site_counts.txt"</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">fail_unless</span><span class="p">(</span><span class="n" style="color: #333;">compare_files</span><span class="p">(</span><span class="s" style="color: #d14;">"../tests/data/small_alignment.constant_site_counts.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"small_alignment.constant_site_counts.txt"</span><span class="p">));</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"small_alignment.constant_site_counts.txt"</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"><span class="n" style="color: #333;">END_TEST</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c"></span>
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272
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"><span class="n" style="color: #333;">Suite</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">snp_sites_suite</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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273
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"><span class="p">{</span></span>
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274
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">Suite</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suite_create</span> <span class="p">(</span><span class="s" style="color: #d14;">"Creating_SNP_Sites"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -302,7 +310,8 @@ Suite * snp_sites_suite (void)</td>
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302
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<td class="diff-line-num new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC310" class="line" lang="c"> <span class="n" style="color: #333;">tcase_add_test</span> <span class="p">(</span><span class="n" style="color: #333;">tc_snp_sites</span><span class="p">,</span> <span class="n" style="color: #333;">valid_phylip_plus_reference</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
303
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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC311" class="line" lang="c"> <span class="n" style="color: #333;">tcase_add_test</span> <span class="p">(</span><span class="n" style="color: #333;">tc_snp_sites</span><span class="p">,</span> <span class="n" style="color: #333;">valid_alignment_with_pure_mode</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC312" class="line" lang="c"> <span class="n" style="color: #333;">tcase_add_test</span> <span class="p">(</span><span class="n" style="color: #333;">tc_snp_sites</span><span class="p">,</span> <span class="n" style="color: #333;">valid_alignment_with_monomorphic_sites</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
305
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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(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="LC305" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">tcase_add_test</span> <span class="p">(</span><span class="n" style="color: #333;">tc_snp_sites</span><span class="p">,</span> <span class="n" style="color: #333;">check_count_constant_sites</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"></span>
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<td class="diff-line-num new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC315" class="line" lang="c"> <span class="n" style="color: #333;">tcase_add_exit_test</span><span class="p">(</span><span class="n" style="color: #333;">tc_snp_sites</span><span class="p">,</span> <span class="n" style="color: #333;">invalid_with_uneven_file_lengths</span><span class="p">,</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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307
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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"uneven_alignment.aln.snp_sites.aln"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC317" class="line" lang="c"> <span class="n" style="color: #333;">suite_add_tcase</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">tc_snp_sites</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/b4b20798e93738f488e415d7cf0bf99f5279bb12#dd9a28dafeb8d6903112bc48ebac2897525e3787"><strong>tests/data/small_alignment.constant_site_counts.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2,2,1,2</span></pre>
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