[med-svn] [Git][med-team/marginphase][master] Add manpages

[Shayan Doust]

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

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