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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/b619c815d8264ed863de396687edd9d2b90949ba">b619c815</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-23T11:47:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Seems rethinkdb is not needed any more
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/a4cc40eb361f1ae767e46a0110148be8fe9656f6">a4cc40eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-23T11:58:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add build time test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/d76804efe99755f48219158cfc93cc44ba59ed79">d76804ef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-23T11:59:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove useless license file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/f319f907a2e625e402e5b4161419643ff18e2f10">f319f907</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-23T15:03:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/e552534c2d5c52c738ab1d67191656de1152a547">e552534c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-23T15:04:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/4e706aef8f86a02e851e639cd4e5b8fe86c6ada9">4e706aef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-24T07:01:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix license
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f8234ce765e214b0332b4c9b8ad3744a5aa6f9e9">
<span class="new-file">
+
debian/augur.1
</span>
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f8234ce765e214b0332b4c9b8ad3744a5aa6f9e9">
<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#f8234ce765e214b0332b4c9b8ad3744a5aa6f9e9"><strong>debian/augur.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH AUGUR "1" "March 2020" "augur 6.4.2" "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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">augur \- pipeline components for real-time virus analysis</span>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B augur</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] {parse,filter,mask,align,tree,refine,ancestral,translate,reconstruct\-sequences,clades,traits,sequence\-traits,lbi,distance,titers,frequencies,export,validate,version,import}</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\&...</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SH DESCRIPTION</span>
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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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Augur: A bioinformatics toolkit for phylogenetic analysis.</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">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</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">{parse,filter,mask,align,tree,refine,ancestral,translate,reconstruct\-sequences,clades,traits,sequence\-traits,lbi,distance,titers,frequencies,export,validate,version,import}</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">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">parse</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Parse delimited fields from FASTA sequence names into</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">a TSV and FASTA file.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">filter</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Filter and subsample a sequence set.</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">mask</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Mask specified sites from a VCF file.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">align</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Align multiple sequences from FASTA.</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">tree</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Build a tree using a variety of methods.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">refine</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Refine an initial tree using sequence metadata.</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">ancestral</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Infer ancestral sequences based on a tree.</span>
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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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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">translate</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Translate gene regions from nucleotides to amino</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">acids.</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">reconstruct\-sequences</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Reconstruct alignments from mutations inferred on the</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">tree</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">clades</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Assign clades to nodes in a tree based on amino\-acid</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">or nucleotide signatures.</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">traits</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Infer ancestral traits based on a tree.</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">sequence\-traits</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Annotate sequences based on amino\-acid or nucleotide</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">signatures.</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">lbi</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Calculate LBI for a given tree and one or more sets of</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">parameters.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">distance</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Calculate the distance between sequences across entire</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">genes or at a predefined subset of sites.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">titers</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Annotate a tree with actual and inferred titer</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">measurements.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.TP</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">frequencies</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">infer frequencies of mutations or clades</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">export</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Export JSON files suitable for visualization with</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">auspice.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.TP</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">validate</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">Validate files related to augur consumption or export.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.TP</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">version</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">Print the version of augur.</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.TP</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">import</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Import analyses into augur pipeline from other systems</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.SS "optional arguments:"</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">augur (6.4.2-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">augur (6.4.2-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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2
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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: #<span class="idiff left right"><bug></span>)</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">954777</span>)</span>
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4
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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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 20 Mar 2020 15:27:37</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 23 Mar 2020 15:03:35</span> +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-biopython <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-jsonschema <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-packaging <!nocheck>,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,8 +34,8 @@ Depends: ${python3:Depends},</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-seaborn (>= 0.6.0),</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> python3-treetime,</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> seqmagick,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> python3-ipdb</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"><span class="idiff left right"># rethinkdb==1.13.0-2,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> python3-ipdb<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"><span class="idiff left right"> python3-bcbio-gff</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: pipeline components for real-time virus analysis</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> The nextstrain project is an attempt to make flexible informatic</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> pipelines and visualization tools to track ongoing pathogen evolution as</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -4,13 +4,13 @@ Source: https://github.com/nextstrain/augur</td>
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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: 2014-2016 Trevor Bedford and Richard Neher</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">License: AGPL-3<span class="idiff left right">+</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: AGPL-3</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: 2017 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">License: AGPL-3<span class="idiff left right">+</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: AGPL-3</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: AGPL-3<span class="idiff left right">+</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: AGPL-3</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> GNU Affero General Public License v3.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Permissions of this strongest copyleft license are conditioned on making</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian<span class="idiff left right">/mans</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>ancestral_reconstruction</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'Reconstructs ancestral sequences and maps mutations to the tree'</span> <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>temporal_signal</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>timetree_inference</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'Reconstructs ancestral sequences and infers a molecular clock tree'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/5fe032a043dfc88140a49ecab50f5401f122585c...4e706aef8f86a02e851e639cd4e5b8fe86c6ada9#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -5,3 +5,7 @@ export LC_ALL=C.UTF-8</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></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"> dh $@ --with python3 --buildsystem=pybuild</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">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> find debian -name LICENSE.txt -delete</span></pre>
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