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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/allelecount">Debian Med / allelecount</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/70cdd6e6ad6017af2fe5d9984efe91ece1bd86f6">70cdd6e6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:40:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/784a76e54726e7791c5c6d9cf8234ae2a0ad0946">784a76e5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:47:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#375be7de03400c79a5833268e0d88149ed14450b">
<span class="new-file">
+
debian/alleleCounter.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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</a>
</li>
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<h4>Changes:</h4>
<li id="375be7de03400c79a5833268e0d88149ed14450b">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb...784a76e54726e7791c5c6d9cf8234ae2a0ad0946#375be7de03400c79a5833268e0d88149ed14450b"><strong>debian/alleleCounter.1</strong></a>
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1
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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 1.47.15.</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 ALLELECOUNTER "1" "May 2020" "alleleCounter 4.1.0" "User Commands"</span>
</pre>
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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">alleleCounter \- NGS copy number algorithms</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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B alleleCounter</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">\fI\,-l loci_file.txt -b sample.bam -o output.txt \/\fR[\fI\,-m int\/\fR] [\fI\,-r ref.fa.fai\/\fR]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Support code for NGS copy number algorithms. Takes a file of locations</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">and a [cr|b]am file and generates a count of coverage of each allele</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">[ACGT] at that location (given any filter settings).</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-l\fR \fB\-\-loci\-file\fR [file]</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">Path to loci file.</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">.TP</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">\fB\-b\fR \fB\-\-hts\-file\fR [file]</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">Path to sample HTS 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">\fB\-o\fR \fB\-\-output\-file\fR [file]</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Path write output file.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SS Optional</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-r\fR \fB\-\-ref\-file\fR [file]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Path to reference fasta index file.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">NB. If cram format is supplied via \fB\-b\fR and the reference listed in the cram header</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">can't be found alleleCounter may fail to work correctly.</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-m\fR \fB\-\-min\-base\-qual\fR [int]</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Minimum base quality [Default: 20].</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-q\fR \fB\-\-min\-map\-qual\fR [int]</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Minimum mapping quality [Default: 35].</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-c\fR \fB\-\-contig\fR [string]</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Limit calling to named contig.</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-d\fR \fB\-\-dense\-snps\fR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Improves performance where many positions are close together</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">\fB\-x\fR \fB\-\-is\-10x\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Enables 10X processing mode.</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">In this mode the HTS input file must be a cellranger produced BAM file. Allele</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">counts are then given on a per\-cellular barcode basis, with each count representing</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">the consensus base for that UMI.</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.IP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">by iterating through bam file rather than using a 'fetch' approach.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-f\fR \fB\-\-required\-flag\fR [int]</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Flag value of reads to retain in allele counting default: [3].</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">N.B. if the proper\-pair flag is are selected, alleleCounter will assume paired\-end</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">and filter out any proper\-pair flagged reads not in F/R orientation. \fB\-F\fR \fB\-\-filtered\-flag\fR [int] Flag value of reads to exclude in allele counting default: [3852].</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-v\fR \fB\-\-version\fR</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Display version number.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">\fB\-h\fR \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Display this usage information.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" 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/allelecount/-/compare/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb...784a76e54726e7791c5c6d9cf8234ae2a0ad0946#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">allelecount (4.1.0-1) <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">allelecount (4.1.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #960345)</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"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 11 May 2020 16:16:46</span> +0200</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">Tue, 12 May 2020 11:41:31</span> +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb...784a76e54726e7791c5c6d9cf8234ae2a0ad0946#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>
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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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4
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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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6
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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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7
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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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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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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10
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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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11
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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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12
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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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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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16
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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>alleleCounter</span>
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17
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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;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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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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19
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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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20
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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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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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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27
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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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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb...784a76e54726e7791c5c6d9cf8234ae2a0ad0946#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/*.1</span></pre>
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