[med-svn] [Git][med-team/allelecount][master] 2 commits: Add manpage

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / allelecount


Commits:
70cdd6e6 by Andreas Tille at 2020-05-12T11:40:53+02:00
Add manpage

- - - - -
784a76e5 by Andreas Tille at 2020-05-12T11:47:04+02:00
Upload to new

- - - - -


4 changed files:

- + debian/alleleCounter.1
- debian/changelog
- + debian/createmanpages
- + debian/manpages


Changes:

=====================================
debian/alleleCounter.1
=====================================
@@ -0,0 +1,62 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH ALLELECOUNTER "1" "May 2020" "alleleCounter 4.1.0" "User Commands"
+.SH NAME
+alleleCounter \- NGS copy number algorithms
+.SH SYNOPSIS
+.B alleleCounter
+\fI\,-l loci_file.txt -b sample.bam -o output.txt \/\fR[\fI\,-m int\/\fR] [\fI\,-r ref.fa.fai\/\fR]
+.SH DESCRIPTION
+Support code for NGS copy number algorithms. Takes a file of locations
+and a [cr|b]am file and generates a count of coverage of each allele
+[ACGT] at that location (given any filter settings).
+.SH OPTIONS
+.TP
+\fB\-l\fR  \fB\-\-loci\-file\fR [file]
+Path to loci file.
+.TP
+\fB\-b\fR  \fB\-\-hts\-file\fR [file]
+Path to sample HTS file.
+.TP
+\fB\-o\fR  \fB\-\-output\-file\fR [file]
+Path write output file.
+.SS Optional
+.TP
+\fB\-r\fR  \fB\-\-ref\-file\fR [file]
+Path to reference fasta index file.
+NB. If cram format is supplied via \fB\-b\fR and the reference listed in the cram header
+.IP
+can't be found alleleCounter may fail to work correctly.
+.TP
+\fB\-m\fR  \fB\-\-min\-base\-qual\fR [int]
+Minimum base quality [Default: 20].
+.TP
+\fB\-q\fR  \fB\-\-min\-map\-qual\fR [int]
+Minimum mapping quality [Default: 35].
+.TP
+\fB\-c\fR  \fB\-\-contig\fR [string]
+Limit calling to named contig.
+.TP
+\fB\-d\fR  \fB\-\-dense\-snps\fR
+Improves performance where many positions are close together
+.TP
+\fB\-x\fR  \fB\-\-is\-10x\fR
+Enables 10X processing mode.
+In this mode the HTS input file must be a cellranger produced BAM file.  Allele
+counts are then given on a per\-cellular barcode basis, with each count representing
+the consensus base for that UMI.
+.IP
+by iterating through bam file rather than using a 'fetch' approach.
+.TP
+\fB\-f\fR  \fB\-\-required\-flag\fR [int]
+Flag value of reads to retain in allele counting default: [3].
+N.B. if the proper\-pair flag is are selected, alleleCounter will assume paired\-end
+and filter out any proper\-pair flagged reads not in F/R orientation. \fB\-F\fR  \fB\-\-filtered\-flag\fR [int]       Flag value of reads to exclude in allele counting default: [3852].
+.TP
+\fB\-v\fR  \fB\-\-version\fR
+Display version number.
+.TP
+\fB\-h\fR  \fB\-\-help\fR
+Display this usage information.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-allelecount (4.1.0-1) UNRELEASED; urgency=medium
+allelecount (4.1.0-1) unstable; urgency=medium
 
   * Initial release (Closes: #960345)
 
- -- Andreas Tille <tille at debian.org>  Mon, 11 May 2020 16:16:46 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 12 May 2020 11:41:31 +0200


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=alleleCounter
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1



View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb...784a76e54726e7791c5c6d9cf8234ae2a0ad0946

-- 
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