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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/marginphase">Debian Med / marginphase</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9">49e3cff9</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-07-01T18:19:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix marginPhase.1 and write new vcfCompare.1
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<h4>2 changed files:</h4>
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<a href="#a487936399429907c5c1b3f18f64b161f7fac9e8">
debian/mans/marginPhase.1
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debian/mans/vcfCompare.1
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<h4>Changes:</h4>
<li id="a487936399429907c5c1b3f18f64b161f7fac9e8">
<a href="https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9#a487936399429907c5c1b3f18f64b161f7fac9e8"><strong>debian/mans/marginPhase.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 1.47.15.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH <span class="idiff left right">USAGE: "1" "June 2020" "usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]</span>" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH <span class="idiff left right">MARGINPHASE "1" "June 2020" "marginPhase</span>" "User Commands"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">usage:</span> \- Simultaneous haplotyping and genotyping</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">marginPhase</span> \- Simultaneous haplotyping and genotyping</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Version: 1.0.0</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,13 +103,13 @@ so reads that aren't in SNP dir are discarded</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN)</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">The full documentation for</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">.B <span class="idiff left right">usage:</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.B <span class="idiff left right">marginPhase</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext">.B info</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">and</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">.B <span class="idiff left right">usage:</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.B <span class="idiff left right">marginPhase</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">.B info <span class="idiff left right">usage:</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.B info <span class="idiff left right">marginPhase</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">should give you access to the complete manual.</span></pre>
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<a href="https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9#fe009b264a6fce631c34ae67e688d085391ebe91"><strong>debian/mans/vcfCompare.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" Text automatically generated by txt2man and modified by hand</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH VCFCOMPARE "01 July 2020" "vcfCompare" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">vcfCompare \- Compares VCF_EVALUATED to VCF_REFERENCE</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B vcfCompare</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[options] \fB-r\fP \fI\,VCF_REFERENCE\/\fR \fB-e\fP \fI\,VCF_EVALUATED\/\fR </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">\fB-h\fP \fB--help\fP : Print this help screen</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB-a\fP \fB--logLevel\fP : Set the log level</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">\fB-r\fP \fB--vcfReference\fP : Specify reference VCF</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB-e\fP \fB--vcfEvaluated\fP : Specify evaluated VCF</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Compares VCF_REFERENCE to VCF_REFERENCE using the following metrics:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP 1. 4</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The concordance of all calls in VCF_REFERENCE compared to VCF_EVALUATED</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.IP 2. 4</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">The concordance of all reference positions in VCF_REFERENCE compared to VCF_EVALUATED</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.IP 3. 4</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">The phasing in VCF_REFERENCE compared to VCF_EVALUATED</span></pre>
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