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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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Commits:
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<strong><a href="https://salsa.debian.org/med-team/marginphase/-/commit/c2cb604453ffb80139ae76e88ce338302500fd2f">c2cb6044</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-06-23T17:12:32+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
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<h4>2 changed files:</h4>
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debian/mans/marginPhase.1
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debian/marginphase.manpages
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<h4>Changes:</h4>
<li id="a487936399429907c5c1b3f18f64b161f7fac9e8">
<a href="https://salsa.debian.org/med-team/marginphase/-/commit/c2cb604453ffb80139ae76e88ce338302500fd2f#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 USAGE: "1" "June 2020" "usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]" "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">usage: \- 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SS "Phases the reads in a BAM file and produces:"</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">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">1) a VCF file giving genotypes and haplotypes.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">2) a SAM file where each read is annotated with haplotype information</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SS "Required arguments:"</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">BAM is the alignment of reads.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">All reads must be aligned to the same contig</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">and be in bam format.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">REFERENCE_FASTA is the reference sequence for the BAM's contig in fasta format.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">PARAMS is the file with marginPhase parameters.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.SS "Default options:"</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-h\fR \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">: Print this help screen</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-o\fR \fB\-\-outputBase\fR</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">: Base output identifier [default = "output"]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">"example" \-> "example.sam", "example.vcf"</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\-a\fR \fB\-\-logLevel\fR</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">: Set the log level [default = info]</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-t\fR \fB\-\-tag\fR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">: Annotate all output reads with this value for the</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\&'mp' tag</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SS "Nucleotide probabilities options:"</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.HP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-s\fR \fB\-\-singleNuclProbDir\fR : Directory of single nucleotide probabilities files</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-S\fR \fB\-\-onlySNP\fR</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">: Use only single nucleotide probabilities information,</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">so reads that aren't in SNP dir are discarded</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.SS "VCF Comparison options:"</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-r\fR \fB\-\-referenceVCF\fR</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">: Reference vcf file for output comparison</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-v\fR \fB\-\-verbose\fR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">: Bitmask controlling outputs</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">1 \- LOG_TRUE_POSITIVES</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">2 \- LOG_FALSE_POSITIVES</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">4 \- LOG_FALSE_NEGATIVES</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.IP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN)</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.PP</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Version: 1.0.0</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.SS "Phases the reads in a BAM file and produces:"</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">1) a VCF file giving genotypes and haplotypes.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">2) a SAM file where each read is annotated with haplotype information</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.SS "Required arguments:"</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">BAM is the alignment of reads.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">All reads must be aligned to the same contig</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.IP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">and be in bam format.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.IP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">REFERENCE_FASTA is the reference sequence for the BAM's contig in fasta format.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">PARAMS is the file with marginPhase parameters.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.SS "Default options:"</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-h\fR \fB\-\-help\fR</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">: Print this help screen</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">\fB\-o\fR \fB\-\-outputBase\fR</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">: Base output identifier [default = "output"]</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">"example" \-> "example.sam", "example.vcf"</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">\fB\-a\fR \fB\-\-logLevel\fR</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">: Set the log level [default = info]</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">\fB\-t\fR \fB\-\-tag\fR</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">: Annotate all output reads with this value for the</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">\&'mp' tag</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.SS "Nucleotide probabilities options:"</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.HP</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">\fB\-s\fR \fB\-\-singleNuclProbDir\fR : Directory of single nucleotide probabilities files</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">\fB\-S\fR \fB\-\-onlySNP\fR</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">: Use only single nucleotide probabilities information,</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">so reads that aren't in SNP dir are discarded</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.SS "VCF Comparison options:"</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
</pre>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">\fB\-r\fR \fB\-\-referenceVCF\fR</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">: Reference vcf file for output comparison</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.TP</span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-v\fR \fB\-\-verbose\fR</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">: Bitmask controlling outputs</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">1 \- LOG_TRUE_POSITIVES</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">2 \- LOG_FALSE_POSITIVES</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">4 \- LOG_FALSE_NEGATIVES</span>
</pre>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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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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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">The full documentation for</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.B usage:</span>
</pre>
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107
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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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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.B info</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">and</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.B usage:</span>
</pre>
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111
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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>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.IP</span>
</pre>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.B info usage:</span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.PP</span>
</pre>
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115
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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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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mans/*.1</span></pre>
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