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<h3>
Sascha Steinbiss pushed to branch master
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/45265acef5591f0b81fa95240e06bd2b4cefc16c">45265ace</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-14T17:30:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix watchfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/fa7d887c715fa196ac6d42997949697bb93043b5">fa7d887c</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-14T17:31:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/fafcb545da06ddb3dc235ef1b0a4da1035c67cbe">fafcb545</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-14T17:31:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.4.0'
Update to upstream version '2.4.0'
with Debian dir add7382a3187fdb173198b31f5c39acd53cd24db</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/412d6141d1a69a8a589d3b26da4c11802e322937">412d6141</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-14T17:33:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/ab456e4206b714976b368b75469c6d6d3d1026ef">ab456e42</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-14T17:36:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mark as UNRELEASED
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
INSTALL
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#3a576e09615c0e19842e5f3ac31e858c9ae7fe41">
src/main.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa"><strong>INSTALL</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Installation</span>
</pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu)<span class="idiff left right">, HomeBrew (OSX) or LinuxBrew</span>.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu)<span class="idiff left right"> or Conda</span>.</span>
</pre>
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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">* Linux - Ubuntu/Debian</span>
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">* Linux - CentOS/RHEL</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">* Linux - using LinuxBrew</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="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">* OSX - using HomeBrew</span>
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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* OSX/Linux - using Bioconda</span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">* OSX/Linux - from source</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">* OSX/Linux - from a release tarball</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,34 +12,18 @@ If you have a recent version of Ubuntu or Debian then you can install it using a</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> apt-get install snp-sites</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">```</span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">## <span class="idiff left right">Linux - CentOS/RHEL</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">The easiest way to install on CentOS/RHEL is to use [LinuxBrew](http://brew.sh/linuxbrew/). Enable EPEL and make sure compilers are installed</span>.</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## <span class="idiff left right">OSX/Linux - using Bioconda</span></span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="plaintext"><span class="idiff left right">Install Conda and install the bioconda channels</span>.</span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">```</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">sudo yum install epel-release gcc gcc-c++ automake ruby-irb</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">```</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Install [LinuxBrew](http://brew.sh/linuxbrew/).</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">```</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">brew tap homebrew/science</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">brew install snp-sites</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">```</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">## Linux - using LinuxBrew</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">Install [LinuxBrew](http://brew.sh/linuxbrew/).</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">```</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">brew tap homebrew/science</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">brew install snp-sites</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">conda config --add channels conda-forge</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">conda config --add channels defaults</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">conda config --add channels r</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">conda config --add channels bioconda</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">conda install snp-sites</span>
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35
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">```</span>
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36
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">## OSX - using HomeBrew</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Install [HomeBrew](http://brew.sh/). It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">```</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">brew tap homebrew/science</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">brew install snp-sites</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">## OSX/Linux - from source</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using <span class="idiff left right">HomeBrew/LinuxBrew</span> instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using <span class="idiff left right">Conda</span> instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites).</span>
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45
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">autoreconf -i -f</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +33,7 @@ sudo make install</td>
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51
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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53
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">## OSX/Linux - from a release tarball</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using <span class="idiff left right">HomeBrew/LinuxBrew</span> instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using <span class="idiff left right">Conda</span> instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).</span>
</pre>
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55
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">tar xzvf snp-sites-x.y.z.tar.gz</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -59,4 +41,8 @@ cd snp-sites-x.y.z</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">./configure</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">make</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">sudo make install</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">```</span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">## All platforms - Docker</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">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="LC48" class="line" lang="plaintext"></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/snp-sites)</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># SNP-sites</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">Rapidly extracts SNPs from a multi-FASTA alignment.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/snp-sites)</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: teal;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000056-brightgreen.svg</span><span class="p">)</span>](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Linux \- Ubuntu/Debian</span><span class="p">](</span><span class="sx" style="color: #d14;">#linux---ubuntudebian</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">OSX/Linux \- using Bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinux---using-bioconda</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">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="LC14" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">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="LC15" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">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="LC17" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">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="LC18" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">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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19
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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: teal;">Output</span><span class="p">](</span><span class="sx" style="color: #d14;">#output</span><span class="p">)</span></span>
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20
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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: teal;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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21
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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: teal;">Feedback/Issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#feedbackissues</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: teal;">Citation</span><span class="p">](</span><span class="sx" style="color: #d14;">#citation</span><span class="p">)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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3
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">The software can be cited as:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">There are a few ways to install SNP-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda. If you encounter an issue when installing SNP-sites please contact your local system administrator. If you encounter a bug please log it <span class="p">[</span><span class="nv" style="color: teal;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/issues</span><span class="p">)</span> or email us at snpsites-help@sanger.ac.uk</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">*</span> Linux - Ubuntu/Debian</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - using Bioconda</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - from source</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - from a release tarball</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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Linux - Ubuntu/Debian</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">If you have a recent version of Ubuntu or Debian then you can install it using apt.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;"> apt-get install snp-sites</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux - using Bioconda</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">Install Conda and install the bioconda channels.</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">```</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;">conda config --add channels conda-forge</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;">conda config --add channels defaults</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;">conda config --add channels r</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;">conda config --add channels bioconda</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;">conda install snp-sites</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">```</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux - from source</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa<span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">ke, autoconf, libtool). Download the software from <span class="p">[</span><span class="nv" style="color: teal;">GitHub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites</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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="sb" style="color: #d14;">autoreconf -i -f</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="sb" style="color: #d14;">./configure</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="sb" style="color: #d14;">make</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;">sudo make install</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="p">```</span></span>
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6
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://dx.doi.org/10.1099/mgen.0.000056</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux - from a release tarball</span></span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa<span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">ke, autoconf, libtool).</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="p">```</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="sb" style="color: #d14;">tar xzvf snp-sites-x.y.z.tar.gz</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="sb" style="color: #d14;">cd snp-sites-x.y.z</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="sb" style="color: #d14;">./configure</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;">make</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="sb" style="color: #d14;">sudo make install</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="p">```</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### All platforms - Docker</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" 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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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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9
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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="sb" style="color: #d14;">Usage: snp-sites [-mvph] [-o output_filename] <file></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="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">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="sb" style="color: #d14;">This program finds snp sites from a multi fasta alignment file.</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -r output internal pseudo reference sequence</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -m output a multi fasta alignment file (default)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -v output a VCF file</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -p output a phylip file</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o specify an output filename</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -h this help message</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -V print version and exit</span></span>
</pre>
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19
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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <file> input alignment file which can optionally be gzipped</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -r output internal pseudo reference sequence</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -m output a multi fasta alignment file (default)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -v output a VCF file</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -p output a phylip file</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o STR specify an output filename [STDOUT]</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -c only output columns containing exclusively ACGT</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -b output monomorphic sites, used for BEAST</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -h this help message</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -V print version and exit</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <file> input alignment file which can optionally be gzipped</span></span>
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20
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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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21
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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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22
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(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="123" style="width: 35px; color: rgba(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">@@ -51,79 +123,20 @@ AGT</td>
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51
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;">snp-sites my_alignment.aln</span></span>
</pre>
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52
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;">snp-sites my_gzipped_alignment.aln.gz</span></span>
</pre>
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53
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Output</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="p">*</span> Multi Fasta Alignment - Similar to the input file but just containing the SNP sites.</span>
</pre>
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54
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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"></span>
</pre>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Multi Fasta Alignment</span></span>
</pre>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown">Similar to the input file but just containing the SNP sites.</span>
</pre>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### VCF</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Relaxed Phylip format</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown">All the SNP sites in a format for RAxML and other tree building applications.</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown">There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu), HomeBrew (OSX) or LinuxBrew.</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"><span class="p">*</span> Linux - Ubuntu/Debian</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="p">*</span> Linux - CentOS/RHEL</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="p">*</span> Linux - using LinuxBrew</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="p">*</span> OSX - using HomeBrew</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - from source</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - from a release tarball</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="p">*</span> Windows/OSX/Linux - using a Virtual Machine</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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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Linux - Ubuntu/Debian</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown">If you have a recent version of Ubuntu or Debian then you can install it using apt.</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;"> apt-get install snp-sites</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown"><span class="p">```</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Linux - CentOS/RHEL</span></span>
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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown">The easiest way to install on CentOS/RHEL is to use <span class="p">[</span><span class="nv" style="color: teal;">LinuxBrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/linuxbrew/</span><span class="p">)</span>. Enable EPEL and make sure compilers are installed.</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>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown"><span class="sb" style="color: #d14;">sudo yum install epel-release gcc gcc-c++ automake ruby-irb</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: teal;">LinuxBrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/linuxbrew/</span><span class="p">)</span>.</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew tap homebrew/science</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;">ln -s $(which gcc) ~/.linuxbrew/bin/gcc-4.4</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;">ln -s $(which g++) ~/.linuxbrew/bin/g++-4.4</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew install snp-sites</span></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"><span class="gu" style="color: #800080; font-weight: 600;">## Linux - using LinuxBrew</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: teal;">LinuxBrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/linuxbrew/</span><span class="p">)</span>.</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew tap homebrew/science</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew install snp-sites</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown"><span class="p">```</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"><span class="p">*</span> VCF - This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.</span>
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100
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX - using HomeBrew</span></span>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: teal;">HomeBrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/</span><span class="p">)</span>. It requires a minimum of Xcode 5.1.1 (xcodebuild -version). Then run:</span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew tap homebrew/science</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
105
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<td class="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown"><span class="sb" style="color: #d14;">brew install snp-sites</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX/Linux - from source</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from <span class="p">[</span><span class="nv" style="color: teal;">GitHub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites</span><span class="p">)</span>.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="p">*</span> Relaxed Phylip format - All the SNP sites in a format for RAxML and other tree building applications.</span>
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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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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="markdown"></span>
</pre>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;">autoreconf -i -f</span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<td class="diff-line-num new_line old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown"><span class="sb" style="color: #d14;">./configure</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown"><span class="sb" style="color: #d14;">make</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;">sudo make install</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown">SNP-sites is free software, licensed under <span class="p">[</span><span class="nv" style="color: teal;">GPLv3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE</span><span class="p">)</span>.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
116
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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<td class="diff-line-num new_line old" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## <span class="idiff left right">OSX/Linux - from a release tarball</span></span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<td class="diff-line-num new_line old" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown"><span class="idiff left right">This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using HomeBrew/LinuxBrew instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool).</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## <span class="idiff left right">Feedback/Issues</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="idiff left">Please report any issues to the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">issues page</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/snp-sites/issues</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> or email snpsites-help@sanger.ac.uk</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
119
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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
138
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"><span class="sb" style="color: #d14;">tar xzvf snp-sites-x.y.z.tar.gz</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"><span class="sb" style="color: #d14;">cd snp-sites-x.y.z</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
123
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;">./configure</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
124
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;">make</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
125
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown"><span class="sb" style="color: #d14;">sudo make install</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
126
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">If you use this software please cite:</span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Windows/OSX/Linux - using a Virtual Machine</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown">A virtual machine (VM) is available containing the software. More details can be found on <span class="p">[</span><span class="nv" style="color: teal;">the Pathogen VM page</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sanger-pathogens.github.io/pathogens-vm/</span><span class="p">)</span>.</span></pre>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown">"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, <span class="p">[</span><span class="nv" style="color: teal;">Microbial Genomics 2(4), (2016)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056</span><span class="p">)</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.<span class="idiff left right">3.3</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.<span class="idiff left right">4.0</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snp-sites (2.4.0-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Adjust watchfile to allow 'v' in version tags.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Update upstream metadata (thanks Steffen Moeller).</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Thu, 14 Jun 2018 17:29:53 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">snp-sites (2.3.3-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Upload to unstable.</span>
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<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">https://github.com/sanger-pathogens/snp-sites/tags \</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> /sanger-pathogens/snp-sites/archive/([.\d]+)\.tar\.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> /sanger-pathogens/snp-sites/archive/<span class="idiff left right">v?</span>([.\d]+)\.tar\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/compare/ea4e0c15388065758cb68902a42d630dad609b03...ab456e4206b714976b368b75469c6d6d3d1026ef#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">@@ -38,7 +38,7 @@ static void print_usage()</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -m output a multi fasta alignment file (default)</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="LC39" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" -v output a VCF 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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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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<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</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="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<span class="idiff left right"> [STDOUT]</span></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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<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;">" -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="LC44" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -62,7 +62,7 @@ static void print_version()</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">multi_fasta_filename</span><span class="p">[</span><span class="n" style="color: #333;">FILENAME_MAX</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">""</span><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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 class="n" style="color: #333;">FILENAME_MAX</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">""</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC65" 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 class="n" style="color: #333;">FILENAME_MAX</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">/dev/stdout</span>"</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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