debian/changelog

-racon (1.3.1-1) UNRELEASED; urgency=medium
+racon (1.3.1-1) unstable; urgency=medium
 
   * Initial release (Closes: #890187)
-  TODO:
-      https://salsa.debian.org/med-team/libbioparser-dev (#901064)
-      https://salsa.debian.org/med-team/libedlib-dev (#901184)
-      https://salsa.debian.org/med-team/rampler (waiting for proper description)
-      https://salsa.debian.org/med-team/spoa (#901145)
-      https://salsa.debian.org/med-team/libthread-pool (#901207)
 
- -- Andreas Tille <tille@debian.org>  Fri, 08 Jun 2018 13:20:51 +0200
+ -- Andreas Tille <tille@debian.org>  Sun, 10 Jun 2018 11:21:59 +0200

debian/control

 Source: racon
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Cédric Lood <cedric.lood@kuleuven.be>,
            Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                libgtest-dev,
@@ -19,13 +19,36 @@ Homepage: https://github.com/isovic/racon
 
 Package: racon
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
 Description: consensus module for raw de novo DNA assembly of long uncorrected reads
  Racon is intended as a standalone consensus module to correct raw
  contigs generated by rapid assembly methods which do not include a
- consensus step, such as Miniasm.
+ consensus step. The goal of Racon is to generate genomic consensus which
+ is of similar or better quality compared to the output generated by
+ assembly methods which employ both error correction and consensus steps,
+ while providing a speedup of several times compared to those methods. It
+ supports data produced by both Pacific Biosciences and Oxford Nanopore
+ Technologies.
+ .
+ Racon can be used as a polishing tool after the assembly with either
+ Illumina data or data produced by third generation of sequencing. The
+ type of data inputed is automatically detected.
+ .
+ Racon takes as input only three files: contigs in FASTA/FASTQ format,
+ reads in FASTA/FASTQ format and overlaps/alignments between the reads
+ and the contigs in MHAP/PAF/SAM format. Output is a set of polished
+ contigs in FASTA format printed to stdout. All input files can be
+ compressed with gzip.
+ .
+ Racon can also be used as a read error-correction tool. In this
+ scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
+ between reads including dual overlaps.
  .
- The goal of Racon is to generate genomic consensus which is of similar
- or better quality compared to the output generated by assembly methods
- which employ both error correction and consensus steps, while
- providing a speedup of several times compared to those m
+ A wrapper script is also available to enable easier usage to the end-
+ user for large datasets. It has the same interface as racon but adds
+ two additional features from the outside. Sequences can be subsampled
+ to decrease the total execution time (accuracy might be lower) while
+ target sequences can be split into smaller chunks and run sequentially
+ to decrease memory consumption. Both features can be run at the same
+ time as well.

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=racon
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+         --name='consensus module for raw de novo DNA assembly of long uncorrected reads' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+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/racon.1

+.TH RACON "1" "June 2018" "racon 1.3.1" "User Commands"
+.SH NAME
+racon \- consensus module for raw de novo DNA assembly of long uncorrected reads
+.SH SYNPOPSIS
+.B racon
+[options ...] <sequences> <overlaps> <target sequences>
+.SH DESCRIPTION
+Racon is intended as a standalone consensus module to correct raw
+contigs generated by rapid assembly methods which do not include a
+consensus step. The goal of Racon is to generate genomic consensus which
+is of similar or better quality compared to the output generated by
+assembly methods which employ both error correction and consensus steps,
+while providing a speedup of several times compared to those methods. It
+supports data produced by both Pacific Biosciences and Oxford Nanopore
+Technologies.
+.P
+Racon can be used as a polishing tool after the assembly with either
+Illumina data or data produced by third generation of sequencing. The
+type of data inputed is automatically detected.
+.P
+Racon takes as input only three files: contigs in FASTA/FASTQ format,
+reads in FASTA/FASTQ format and overlaps/alignments between the reads
+and the contigs in MHAP/PAF/SAM format. Output is a set of polished
+contigs in FASTA format printed to stdout. All input files can be
+compressed with gzip.
+.P
+Racon can also be used as a read error-correction tool. In this
+scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
+between reads including dual overlaps.
+.P
+A wrapper script is also available to enable easier usage to the end-
+user for large datasets. It has the same interface as racon but adds
+two additional features from the outside. Sequences can be subsampled
+to decrease the total execution time (accuracy might be lower) while
+target sequences can be split into smaller chunks and run sequentially
+to decrease memory consumption. Both features can be run at the same
+time as well.
+.SH OPTIONS
+.HP
+<sequences>
+.IP
+input file in FASTA/FASTQ format (can be compressed with gzip)
+containing sequences used for correction
+.HP
+<overlaps>
+.IP
+input file in MHAP/PAF/SAM format (can be compressed with gzip)
+containing overlaps between sequences and target sequences
+.HP
+<target sequences>
+.IP
+input file in FASTA/FASTQ format (can be compressed with gzip)
+containing sequences which will be corrected
+.SS optional
+.HP
+\fB\-u\fR, \fB\-\-include\-unpolished\fR
+.IP
+output unpolished target sequences
+.HP
+\fB\-f\fR, \fB\-\-fragment\-correction\fR
+.IP
+perform fragment correction instead of contig polishing
+(overlaps file should contain dual/self overlaps!)
+.HP
+\fB\-w\fR, \fB\-\-window\-length\fR <int>
+.IP
+default: 500
+size of window on which POA is performed
+.HP
+\fB\-q\fR, \fB\-\-quality\-threshold\fR <float>
+.IP
+default: 10.0
+threshold for average base quality of windows used in POA
+.HP
+\fB\-e\fR, \fB\-\-error\-threshold\fR <float>
+.IP
+default: 0.3
+maximum allowed error rate used for filtering overlaps
+.HP
+\fB\-m\fR, \fB\-\-match\fR <int>
+.IP
+default: 5
+score for matching bases
+.HP
+\fB\-x\fR, \fB\-\-mismatch\fR <int>
+.IP
+default: \fB\-4\fR
+score for mismatching bases
+.HP
+\fB\-g\fR, \fB\-\-gap\fR <int>
+.IP
+default: \fB\-8\fR
+gap penalty (must be negative)
+.HP
+\fB\-t\fR, \fB\-\-threads\fR <int>
+.IP
+default: 1
+number of threads
+.HP
+\fB\-\-version\fR
+.IP
+prints the version number
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+prints the usage
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.