Shayan Doust pushed to branch master at Debian Med / marginphase
Commits: c2cb6044 by Shayan Doust at 2020-06-23T17:12:32+01:00 Add manpages - - - - - 2 changed files: - + debian/mans/marginPhase.1 - + debian/marginphase.manpages Changes: ===================================== debian/mans/marginPhase.1 ===================================== @@ -0,0 +1,115 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. +.TH USAGE: "1" "June 2020" "usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]" "User Commands" +.SH NAME +usage: \- Simultaneous haplotyping and genotyping +.SH DESCRIPTION +usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options] +Version: 1.0.0 +.SS "Phases the reads in a BAM file and produces:" +.IP +1) a VCF file giving genotypes and haplotypes. +2) a SAM file where each read is annotated with haplotype information +.SS "Required arguments:" +.TP +BAM is the alignment of reads. +All reads must be aligned to the same contig +.IP +and be in bam format. +.IP +REFERENCE_FASTA is the reference sequence for the BAM's contig in fasta format. +PARAMS is the file with marginPhase parameters. +.SS "Default options:" +.TP +\fB\-h\fR \fB\-\-help\fR +: Print this help screen +.TP +\fB\-o\fR \fB\-\-outputBase\fR +: Base output identifier [default = "output"] +"example" \-> "example.sam", "example.vcf" +.TP +\fB\-a\fR \fB\-\-logLevel\fR +: Set the log level [default = info] +.TP +\fB\-t\fR \fB\-\-tag\fR +: Annotate all output reads with this value for the +\&'mp' tag +.SS "Nucleotide probabilities options:" +.HP +\fB\-s\fR \fB\-\-singleNuclProbDir\fR : Directory of single nucleotide probabilities files +.TP +\fB\-S\fR \fB\-\-onlySNP\fR +: Use only single nucleotide probabilities information, +so reads that aren't in SNP dir are discarded +.SS "VCF Comparison options:" +.TP +\fB\-r\fR \fB\-\-referenceVCF\fR +: Reference vcf file for output comparison +.TP +\fB\-v\fR \fB\-\-verbose\fR +: Bitmask controlling outputs +1 \- LOG_TRUE_POSITIVES +2 \- LOG_FALSE_POSITIVES +4 \- LOG_FALSE_NEGATIVES +.IP +example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN) +.PP +Version: 1.0.0 +.SS "Phases the reads in a BAM file and produces:" +.IP +1) a VCF file giving genotypes and haplotypes. +2) a SAM file where each read is annotated with haplotype information +.SS "Required arguments:" +.TP +BAM is the alignment of reads. +All reads must be aligned to the same contig +.IP +and be in bam format. +.IP +REFERENCE_FASTA is the reference sequence for the BAM's contig in fasta format. +PARAMS is the file with marginPhase parameters. +.SS "Default options:" +.TP +\fB\-h\fR \fB\-\-help\fR +: Print this help screen +.TP +\fB\-o\fR \fB\-\-outputBase\fR +: Base output identifier [default = "output"] +"example" \-> "example.sam", "example.vcf" +.TP +\fB\-a\fR \fB\-\-logLevel\fR +: Set the log level [default = info] +.TP +\fB\-t\fR \fB\-\-tag\fR +: Annotate all output reads with this value for the +\&'mp' tag +.SS "Nucleotide probabilities options:" +.HP +\fB\-s\fR \fB\-\-singleNuclProbDir\fR : Directory of single nucleotide probabilities files +.TP +\fB\-S\fR \fB\-\-onlySNP\fR +: Use only single nucleotide probabilities information, +so reads that aren't in SNP dir are discarded +.SS "VCF Comparison options:" +.TP +\fB\-r\fR \fB\-\-referenceVCF\fR +: Reference vcf file for output comparison +.TP +\fB\-v\fR \fB\-\-verbose\fR +: Bitmask controlling outputs +1 \- LOG_TRUE_POSITIVES +2 \- LOG_FALSE_POSITIVES +4 \- LOG_FALSE_NEGATIVES +.IP +example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN) +.SH "SEE ALSO" +The full documentation for +.B usage: +is maintained as a Texinfo manual. If the +.B info +and +.B usage: +programs are properly installed at your site, the command +.IP +.B info usage: +.PP +should give you access to the complete manual. ===================================== debian/marginphase.manpages ===================================== @@ -0,0 +1 @@ +mans/*.1 View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/c2cb604453ffb80139ae76e88ce338302500fd2f -- View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/c2cb604453ffb80139ae76e88ce338302500fd2f You're receiving this email because of your account on salsa.debian.org.
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