Andreas Tille pushed to branch master at Debian Med / lighter
Commits:
44de835e by Andreas Tille at 2020-05-27T22:36:59+02:00
ITP bug
- - - - -
b8ae51a7 by Andreas Tille at 2020-05-27T22:39:03+02:00
Add manpage
- - - - -
ebdc5fb9 by Andreas Tille at 2020-05-27T22:41:59+02:00
Upload to new
- - - - -
4 changed files:
- debian/changelog
- + debian/createmanpages
- + debian/lighter.1
- + debian/manpages
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-lighter (1.1.2-1) UNRELEASED; urgency=medium
+lighter (1.1.2-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #961665)
- -- Andreas Tille <ti...@debian.org> Wed, 27 May 2020 15:51:30 +0200
+ -- Andreas Tille <ti...@debian.org> Wed, 27 May 2020 22:39:10 +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 $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${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/lighter.1
=====================================
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH LIGHTER "1" "May 2020" "lighter 1.1.2" "User Commands"
+.SH NAME
+lighter \- fast and memory-efficient sequencing error corrector
+.SH SYNOPSIS
+.B lighter
+[\fI\,OPTIONS\/\fR]
+.SH DESCRIPTION
+Lighter is a fast, memory-efficient tool for correcting sequencing
+errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom
+filters, one holding a sample of the input k-mers and the other holding
+k-mers likely to be correct. As long as the sampling fraction is
+adjusted in inverse proportion to the depth of sequencing, Bloom filter
+size can be held constant while maintaining near-constant accuracy.
+Lighter is parallelized, uses no secondary storage, and is both faster
+and more memory-efficient than competing approaches while achieving
+comparable accuracy.
+.SH OPTIONS:
+.SS Required parameters:
+.TP
+\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use
multiple \fB\-r\fR to specifiy multiple sequence files
+The file can be fasta and fastq, and can be gzip'ed with extension *.gz.
+When the input file is *.gz, the corresponding output file will also be
gzip'ed.
+.TP
+\fB\-k\fR kmer_length genome_size alpha: (see README for information on
setting alpha)
+or
+.HP
+\fB\-K\fR kmer_length genom_size: in this case, the genome size should be
relative accurate.
+.SS "Other parameters:"
+.HP
+\fB\-od\fR output_file_directory: (default: ./)
+.HP
+\fB\-t\fR num_of_threads: number of threads to use (default: 1)
+.HP
+\fB\-maxcor\fR INT: the maximum number of corrections within a 20bp window
(default: 4)
+.HP
+\fB\-trim\fR: allow trimming (default: false)
+.HP
+\fB\-discard\fR: discard unfixable reads. Will LOSE paired\-end matching when
discarding (default: false)
+.HP
+\fB\-noQual\fR: ignore the quality socre (default: false)
+.HP
+\fB\-newQual\fR ascii_quality_score: set the quality for the bases corrected
to the specified score (default: not used)
+.HP
+\fB\-saveTrustedKmers\fR file: save the trusted kmers to specified file then
stop (default: not used)
+.HP
+\fB\-loadTrustedKmers\fR file: directly get solid kmers from specified file
(default: not used)
+.HP
+\fB\-zlib\fR compress_level: set the compression level(0\-9) of gzip (default:
1)
+.HP
+\fB\-h\fR: print the help message and quit
+.HP
+\fB\-v\fR: print the version information and quit
+.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/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab:
https://salsa.debian.org/med-team/lighter/-/compare/8cdccd4b023e2f0c023895b58e4298a609d116ba...ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41
--
View it on GitLab:
https://salsa.debian.org/med-team/lighter/-/compare/8cdccd4b023e2f0c023895b58e4298a609d116ba...ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41
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