[med-svn] [Git][med-team/covtobed][master] Manpages for covtobed

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / covtobed


Commits:
43ec387a by Shayan Doust at 2020-05-31T18:08:16+01:00
Manpages for covtobed

- - - - -


2 changed files:

- + debian/covtobed.manpages
- + debian/mans/covtobed.1


Changes:

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debian/covtobed.manpages
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+debian/mans/covtobed.1


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debian/mans/covtobed.1
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+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH COVTOBED "1" "May 2020" "covtobed 1.1.2" "User Commands"
+.SH NAME
+covtobed \- a tool to generate BED coverage tracks from BAM files
+.SH SYNOPSIS
+.B covtobed
+[\fI\,options\/\fR] [\fI\,BAM\/\fR]...
+.SH DESCRIPTION
+Reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-physical\-coverage\fR
+compute physical coverage (needs paired alignments in input)
+.TP
+\fB\-q\fR MINQ, \fB\-\-min\-mapq\fR=\fI\,MINQ\/\fR
+skip alignments whose mapping quality is less than MINQ
+(default: 0)
+.TP
+\fB\-m\fR MINCOV, \fB\-\-min\-cov\fR=\fI\,MINCOV\/\fR
+print BED feature only if the coverage is bigger than
+(or equal to) MINCOV (default: 0)
+.TP
+\fB\-x\fR MAXCOV, \fB\-\-max\-cov\fR=\fI\,MAXCOV\/\fR
+print BED feature only if the coverage is lower than
+MAXCOV (default: 100000)
+.TP
+\fB\-l\fR MINLEN, \fB\-\-min\-len\fR=\fI\,MINLEN\/\fR
+print BED feature only if its length is bigger (or equal
+to) than MINLELN (default: 1)
+.TP
+\fB\-d\fR, \fB\-\-discard\-invalid\-alignments\fR
+skip duplicates, failed QC, and non primary alignment,
+minq>0 (or user\-defined if higher) (default: 0)
+.TP
+\fB\-\-output\-strands\fR
+output coverage and stats separately for each strand
+.TP
+\fB\-\-format\fR=\fI\,CHOICE\/\fR
+output format
+.SH COPYRIGHT
+Copyright \(co 2014\-2019 Giovanni Birolo and Andrea Telatin
+https://github.com/telatin/covtobed \- License MIT.
+.br
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+.SH "SEE ALSO"
+The full documentation for
+.B covtobed
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B covtobed
+programs are properly installed at your site, the command
+.IP
+.B info covtobed
+.PP
+should give you access to the complete manual.



View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/commit/43ec387a5019a2ba4d4d8353ad67d1ee1b101348

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