debian/changelog

-umis (1.0.3-1) UNRELEASED; urgency=medium
+umis (1.0.3-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #926995)
 
- -- Andreas Tille <tille@debian.org>  Sat, 13 Apr 2019 07:12:50 +0200
+ -- Andreas Tille <tille@debian.org>  Sat, 13 Apr 2019 10:35:26 +0200

debian/createmanpages

+#!/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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --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

+debian/*.1

debian/umis-examples.lintian-overrides

+# These files are needed in compressed and uncompressed form
+umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/CEL-Seq/SRP036633_1.fastq.gz
+umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/CEL-Seq/SRP036633_2.fastq.gz
+umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/tagcount/cb-histogram.txt.gz
+

debian/umis.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UMIS "1" "April 2019" "umis 1.0.3" "User Commands"
+.SH NAME
+umis \- tools for processing UMI RNA-tag data
+.SH SYNOPSIS
+.B umis
+[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]...
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+Show this message and exit.
+.SS "Commands:"
+.TP
+add_uid
+Adds UID:[samplebc cellbc umi] to readname for...
+.TP
+bamtag
+Convert a BAM/SAM with fastqtransformed read names
+to...
+.TP
+cb_filter
+Filters reads with non\-matching barcodes Expects...
+.TP
+cb_histogram
+Counts the number of reads for each cellular barcode...
+.TP
+demultiplex_cells
+Demultiplex a fastqtransformed FASTQ file into a...
+.TP
+demultiplex_samples
+Demultiplex a fastqtransformed FASTQ file into a...
+.TP
+fastqtransform
+Transform input reads to the tagcounts compatible...
+.TP
+fasttagcount
+Count up evidence for tagged molecules, this...
+.TP
+kallisto
+Convert fastqtransformed file to output format...
+.TP
+mb_filter
+Filters umis with non\-ACGT bases Expects formatted...
+.TP
+sb_filter
+Filters reads with non\-matching sample barcodes...
+.TP
+sparse
+Convert a CSV file to a sparse matrix with rows and...
+.TP
+subset_bamfile
+Subset a SAM/BAM file, keeping only alignments from...
+.TP
+tagcount
+Count up evidence for tagged molecules
+.TP
+umi_histogram
+Counts the number of reads for each UMI Expects...
+.IP
+version
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.