[med-svn] [Git][med-team/pilon][master] 2 commits: Add manpage
Andreas Tille
gitlab at salsa.debian.org
Fri Aug 3 09:38:16 BST 2018
Andreas Tille pushed to branch master at Debian Med / pilon
Commits:
1e0a80e1 by Andreas Tille at 2018-08-03T06:36:07Z
Add manpage
- - - - -
c74f52df by Andreas Tille at 2018-08-03T08:37:56Z
Missuse ITP for pilon-non-free
- - - - -
4 changed files:
- debian/changelog
- + debian/createmanpages
- + debian/manpages
- + debian/pilon.1
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-pilon (1.22+dfsg-1) UNRELEASED; urgency=medium
+pilon (1.22+dfsg-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #903911)
- -- Andreas Tille <tille at debian.org> Thu, 23 Feb 2017 16:48:18 +0100
+ -- Andreas Tille <tille at debian.org> Fri, 03 Aug 2018 10:37:51 +0200
=====================================
debian/createmanpages
=====================================
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,31 @@
+#!/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: *//'`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=pilon
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+sed -i \
+ -e 's/specifed/specified/' \
+ -e 's/minumum/minimum/' \
+ $MANDIR/${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
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/pilon.1
=====================================
--- /dev/null
+++ b/debian/pilon.1
@@ -0,0 +1,213 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+.TH PILON "1" "June 2018" "pilon 1.22" "User Commands"
+.SH NAME
+pilon \- automated genome assembly improvement and variant detection tool
+.SH SYNOPSIS
+.B pilon
+\fB\-\-genome\fR genome.fasta [\-\-frags frags.bam] [\-\-jumps jumps.bam] [\-\-unpaired unpaired.bam]
+[...other options...]
+.SH DESCRIPTION
+Pilon is a software tool which can be used to:
+.IP \[bu] 2
+Automatically improve draft assemblies
+.IP \[bu]
+Find variation among strains, including large event detection
+.P
+Pilon requires as input a FASTA file of the genome along with one or more
+BAM files of reads aligned to the input FASTA file. Pilon uses read
+alignment analysis to identify inconsistencies between the input genome and
+the evidence in the reads. It then attempts to make improvements to the
+input genome, including:
+.IP \[bu] 2
+Single base differences
+.IP \[bu]
+Small indels
+.IP \[bu]
+Larger indel or block substitution events
+.IP \[bu]
+Gap filling
+.IP \[bu]
+Identification of local misassemblies, including optional opening of new gaps
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+.IP
+for option details
+.SS INPUTS
+.IP
+\fB\-\-genome\fR genome.fasta
+.IP
+The input genome we are trying to improve, which must be the reference used
+for the bam alignments. At least one of \fB\-\-frags\fR or \fB\-\-jumps\fR must also be given.
+.IP
+\fB\-\-frags\fR frags.bam
+.IP
+A bam file consisting of fragment paired\-end alignments, aligned to the \fB\-\-genome\fR
+argument using bwa or bowtie2. This argument may be specified more than once.
+.IP
+\fB\-\-jumps\fR jumps.bam
+.IP
+A bam file consisting of jump (mate pair) paired\-end alignments, aligned to the
+\fB\-\-genome\fR argument using bwa or bowtie2. This argument may be specified more than once.
+.IP
+\fB\-\-unpaired\fR unpaired.bam
+.IP
+A bam file consisting of unpaired alignments, aligned to the \fB\-\-genome\fR argument
+using bwa or bowtie2. This argument may be specified more than once.
+.IP
+\fB\-\-bam\fR any.bam
+.IP
+A bam file of unknown type; Pilon will scan it and attempt to classify it as one
+of the above bam types.
+.SS OUTPUTS
+.IP
+\fB\-\-output\fR prefix
+.IP
+Prefix for output files
+.IP
+\fB\-\-outdir\fR directory
+.IP
+Use this directory for all output files.
+.IP
+\fB\-\-changes\fR
+.IP
+If specified, a file listing changes in the <output>.fasta will be generated.
+.IP
+\fB\-\-vcf\fR
+.IP
+If specified, a vcf file will be generated
+.IP
+\fB\-\-vcfqe\fR
+.IP
+If specified, the VCF will contain a QE (quality\-weighted evidence) field rather
+than the default QP (quality\-weighted percentage of evidence) field.
+.IP
+\fB\-\-tracks\fR
+.IP
+This options will cause many track files (*.bed, *.wig) suitable for viewing in
+a genome browser to be written.
+.SS CONTROL
+.IP
+\fB\-\-variant\fR
+.IP
+Sets up heuristics for variant calling, as opposed to assembly improvement;
+equivalent to "\-\-vcf \fB\-\-fix\fR all,breaks".
+.IP
+\fB\-\-chunksize\fR
+.IP
+Input FASTA elements larger than this will be processed in smaller pieces not to
+exceed this size (default 10000000).
+.IP
+\fB\-\-diploid\fR
+.IP
+Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
+.IP
+\fB\-\-fix\fR fixlist
+.IP
+A comma\-separated list of categories of issues to try to fix:
+.IP
+"snps": try to fix individual base errors;
+"indels": try to fix small indels;
+"gaps": try to fill gaps;
+"local": try to detect and fix local misassemblies;
+"all": all of the above (default);
+"bases": shorthand for "snps" and "indels" (for back compatibility);
+"none": none of the above; new fasta file will not be written.
+.IP
+The following are experimental fix types:
+.IP
+"amb": fix ambiguous bases in fasta output (to most likely alternative);
+"breaks": allow local reassembly to open new gaps (with "local");
+"circles": try to close circlar elements when used with long corrected reads;
+"novel": assemble novel sequence from unaligned non\-jump reads.
+.IP
+\fB\-\-dumpreads\fR
+.IP
+Dump reads for local re\-assemblies.
+.IP
+\fB\-\-duplicates\fR
+.IP
+Use reads marked as duplicates in the input BAMs (ignored by default).
+.IP
+\fB\-\-iupac\fR
+.IP
+Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
+.IP
+\fB\-\-nonpf\fR
+.IP
+Use reads which failed sequencer quality filtering (ignored by default).
+.IP
+\fB\-\-targets\fR targetlist
+.IP
+Only process the specified target(s).
+Targets are comma\-separated, and each target
+.IP
+is a fasta element name optionally followed by a base range.
+Example: "scaffold00001,scaffold00002:10000\-20000" would result in processing all of
+scaffold00001 and coordinates 10000\-20000 of scaffold00002.
+If "targetlist" is the name of a file, each line will be treated as a target
+specification.
+.IP
+\fB\-\-threads\fR
+.IP
+Degree of parallelism to use for certain processing (default 1). Experimental.
+.IP
+\fB\-\-verbose\fR
+.IP
+More verbose output.
+.IP
+\fB\-\-debug\fR
+.IP
+Debugging output (implies verbose).
+.IP
+\fB\-\-version\fR
+.IP
+Print version string and exit.
+.SS HEURISTICS:
+.IP
+\fB\-\-defaultqual\fR qual
+.IP
+Assumes bases are of this quality if quals are no present in input BAMs (default 15).
+.IP
+\fB\-\-flank\fR nbases
+.IP
+Controls how much of the well\-aligned reads will be used; this many bases at each
+end of the good reads will be ignored (default 10).
+.IP
+\fB\-\-gapmargin\fR
+.IP
+Closed gaps must be within this number of bases of true size to be closed (100000)
+.IP
+\fB\-\-K\fR
+.IP
+Kmer size used by internal assembler (default 47).
+.IP
+\fB\-\-mindepth\fR depth
+.IP
+Variants (snps and indels) will only be called if there is coverage of good pairs
+at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
+fraction < 1, then minimum depth is computed by multiplying this value by the mean
+coverage for the region, with a minimum value of 5 (default 0.1: min depth to call
+is 10% of mean coverage or 5, whichever is greater).
+.IP
+\fB\-\-mingap\fR
+.IP
+Minimum size for unclosed gaps (default 10)
+.IP
+\fB\-\-minmq\fR
+.IP
+Minimum alignment mapping quality for a read to count in pileups (default 0)
+.IP
+\fB\-\-minqual\fR
+.IP
+Minimum base quality to consider for pileups (default 0)
+.IP
+\fB\-\-nostrays\fR
+.IP
+Skip making a pass through the input BAM files to identify stray pairs, that is,
+those pairs in which both reads are aligned but not marked valid because they have
+inconsistent orientation or separation. Identifying stray pairs can help fill gaps
+and assemble larger insertions, especially of repeat content. However, doing so
+sometimes consumes considerable memory.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577
--
View it on GitLab: https://salsa.debian.org/med-team/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577
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