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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sweed">Debian Med / sweed</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153">5aa75c85</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-07-04T00:54:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import Debian changes 3.2.1+dfsg-1
sweed (3.2.1+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #902960)
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="new-file">
+
debian/README.source
</span>
</a>
</li>
<li class="file-stats">
<a href="#56685794bf218368316aaafb4123584221ffa17c">
<span class="new-file">
+
debian/SweeD.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
<span class="new-file">
+
debian/changelog
</span>
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="new-file">
+
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<span class="new-file">
+
debian/control
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</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<span class="new-file">
+
debian/copyright
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
<span class="new-file">
+
debian/rules
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</li>
<li class="file-stats">
<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">
<span class="new-file">
+
debian/source/format
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</li>
<li class="file-stats">
<a href="#04485081f77c8f6550c395d9bbd7234f8c11fbdd">
<span class="new-file">
+
debian/sweed.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
+
debian/upstream/metadata
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">The unfortunate original tarball contained object files.</span></pre>
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<br>
</li>
<li id="56685794bf218368316aaafb4123584221ffa17c">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#56685794bf218368316aaafb4123584221ffa17c"><strong>debian/SweeD.1</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SWEED "1" "July 2018" "SweeD " "User Commands"</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">SweeD \- Assess SNPs for their contribution to genetic drift</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">SweeD version 3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2013.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">SweeD | SweeD\-P | SweeD\-C | SweeD\-P\-C</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-name\fR runName</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-input\fR inputFile</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.HP</span>
</pre>
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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">\fB\-grid\fR gridNumber</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">[\-folded]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">[\-monomorphic]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">[\-strictPolymorphic]</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">[\-isfs inputSFS]</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">[\-osfs outputSFS]</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">[\-osf outputSF]</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">[\-threads threadNumber]</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">[\-checkpoint checkpointInterval]</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">[\-eN timeT sizeX]</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">[\-G rateG]</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">[\-s sequences]</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">[\-h|\-help]</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">[\-v|version]</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-name\fR <STRING></span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Specifies a name for the run and the output files.</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-input\fR <STRING></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Specifies the name of the input alignment file.</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Supported file formats: SF (Sweep Finder) format.</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-grid\fR <INTEGER></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Specifies the number of positions in the alignment where the CLR will be computed.</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-folded\fR</span>
</pre>
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42
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Considers the SFS folded (the ancestral and derived states can not be distinguished).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-monomorphic\fR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Includes the monomorphic sites in the analysis. The default action is to discard them.</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-strictPolymorphic\fR</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Does not include *potential monomorphic* sites in the analysis. These are sites where for some sequences the state is missing and the remaining are monomorphic.</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-isfs\fR <STRING></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Specifies the name of the input SFS file.</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-osfs\fR <STRING></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Specifies the name of the output SFS file.</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-osf\fR <STRING></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Specifies the name of the output SF file.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-threads\fR <INTEGER></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Specifies the number of threads.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-checkpoint\fR <INTEGER></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Specifies the checkpoint interval in seconds (default: 3600).</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">\fB\-eN\fR <FLOAT> <FLOAT></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Sets population size to sizeX*N0 at time timeT, where N0 is the present\-day population size.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-G\fR <FLOAT></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Sets the growth rate of the population size at time 0. The growth rate continues to be exponential until</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">the \fB\-eN\fR command specifies a constant population size.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-s\fR <INTEGER></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Specifies the number of sequences when no input file is provided.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">\fB\-h\fR|\-help</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Displays this help message.</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sweed (3.2.1+dfsg-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #902960)</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 04 Jul 2018 00:25:27 +0200</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: sweed</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Maintainer: Steffen Moeller <moeller@debian.org></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Build-Depends: debhelper (>= 11)</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Homepage: https://sco.h-its.org/exelixis/web/software/sweed/</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sweed</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sweed.git</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Package: sweed</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Description: assessment of SNPs for their evolutionary advantage</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Biological sequences are available in ever increasing abundance across</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ever larger populations for ever increasing fractions of the genome. This</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> tool sorts the SNPs for their active or passive contribution to a genetic</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> drift, i.e. to see particular sequences at a higher fraction over time.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: SweeD</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://sco.h-its.org/exelixis/web/software/sweed/index.html</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 2011-12 Nikolaos Alachiotis and Pavlos Pavlidis</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: GPL-2.0+</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">Files: debian/*</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2018 Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: GPL-2.0+</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: GPL-2.0+</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> the Free Software Foundation; either version 2 of the License, or</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> (at your option) any later version.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> .</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> This package is distributed in the hope that it will be useful,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> GNU General Public License for more details.</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"> You should have received a copy of the GNU General Public License</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> .</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU General</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".</span></pre>
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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/SweeD.1</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># See debhelper(7) (uncomment to enable)</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># output every command that modifies files on the build system.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">#export DH_VERBOSE = 1</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">%:</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh $@</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">override_dh_auto_build:</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> $(MAKE) -f Makefile.gcc $*</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" 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">override_dh_auto_clean:</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh_auto_clean</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> rm -f *.o *~ SweeD</span></pre>
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<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#04485081f77c8f6550c395d9bbd7234f8c11fbdd"><strong>debian/sweed.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">SweeD</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sweed/commit/5aa75c857256e069a2b0be8811c1ec70c9e2f153#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Author: ></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Pavlos Pavlidis and Daniel Živković and Alexandros Stamatakis and</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Nikolaos Alachiotis</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Title: ></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> of Genomes</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Journal: Molecular Biology and Evolution</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Volume: 30</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Issue: 9</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Day: 1</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Month: 9</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Year: 2013</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Pages: 2224–2234</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> DOI: 10.1093/molbev/mst112</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> URL: https://academic.oup.com/mbe/article/30/9/2224/999783</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ePrint: ></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> https://academic.oup.com/mbe/article-pdf/30/9/2224/13175153/mst112.pdf</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> - Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: OMICS_08598</span></pre>
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