[med-svn] r13068 - trunk/packages/flexbar/trunk/debian

Andreas Tille tille at alioth.debian.org
Sat Feb 23 11:34:50 UTC 2013 

Author: tille
Date: 2013-02-23 11:34:50 +0000 (Sat, 23 Feb 2013)
New Revision: 13068

Added:
   trunk/packages/flexbar/trunk/debian/flexbar.1
   trunk/packages/flexbar/trunk/debian/manpages
Log:
Manpage for flexbar


Added: trunk/packages/flexbar/trunk/debian/flexbar.1
===================================================================
--- trunk/packages/flexbar/trunk/debian/flexbar.1	                        (rev 0)
+++ trunk/packages/flexbar/trunk/debian/flexbar.1	2013-02-23 11:34:50 UTC (rev 13068)
@@ -0,0 +1,261 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
+.TH FLEXBAR "1" "February 2013" "flexbar version 2.32" "User Commands"
+.SH NAME
+flexbar \- flexible barcode and adapter removal for sequencing platforms
+.SH SYNOPSIS
+.IP
+flexbar \fB\-t\fR target \fB\-f\fR format \fB\-r\fR
+reads [\-b barcodes] [\-a adapters]
+[options]
+.PP
+.SH OPTIONS
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Display this help message
+.HP
+\fB\-v\fR, \fB\-\-version\fR
+.IP
+Display program version
+.HP
+\fB\-c\fR, \fB\-\-cite\fR
+.IP
+View citation information
+.IP
+Basic options:
+.HP
+\fB\-n\fR, \fB\-\-threads\fR NUM
+.IP
+Number of threads, default:
+1
+.HP
+\fB\-t\fR, \fB\-\-target\fR STR
+.IP
+Prefix for output file names
+.HP
+\fB\-r\fR, \fB\-\-reads\fR FILE
+.IP
+Input file with reads, that
+may contain barcodes
+.HP
+\fB\-p\fR, \fB\-\-reads2\fR FILE
+.IP
+Second input file for paired
+read scenario
+.HP
+\fB\-f\fR, \fB\-\-format\fR STR
+.IP
+Input format of reads:
+csfasta, csfastq, fasta,
+fastq, fastq\-sanger,
+fastq\-solexa, fastq\-i1.3,
+fastq\-i1.5, fastq\-i1.8
+(illumina 1.8+)
+.IP
+Barcode detection:
+.HP
+\fB\-b\fR, \fB\-\-barcodes\fR FILE
+.IP
+Fasta file with barcodes,
+specify (br) to use separate
+barcode reads
+.HP
+\fB\-br\fR, \fB\-\-barcode\-reads\fR FILE
+.IP
+Fasta or fastq file with
+separate barcode reads, if
+not within reads
+.HP
+\fB\-be\fR, \fB\-\-barcode\-trim\-end\fR STR
+.IP
+Type of barcoding within
+reads, see section trim\-end
+modes, default: ANY
+.HP
+\fB\-bn\fR, \fB\-\-barcode\-tail\-length\fR NUM
+.IP
+Number of bases for tail
+trim\-end types, default:
+barcode length
+.HP
+\fB\-bo\fR, \fB\-\-barcode\-min\-overlap\fR NUM
+.IP
+Minimum overlap of barcode
+and read, default: barcode
+length
+.HP
+\fB\-bt\fR, \fB\-\-barcode\-threshold\fR NUM
+.IP
+Allowed mismatches and
+indels per 10 bases for
+barcode, default: 1.0
+.HP
+\fB\-bk\fR, \fB\-\-barcode\-keep\fR
+.IP
+Keep barcodes within reads
+instead of removal
+.HP
+\fB\-ba\fR, \fB\-\-barcode\-tag\-length\fR NUM
+.IP
+Use random code with given
+size upstream barcode for
+read tagging
+.HP
+\fB\-bm\fR, \fB\-\-barcode\-match\fR NUM
+.IP
+Match score, default: 1
+.HP
+\fB\-bi\fR, \fB\-\-barcode\-mismatch\fR NUM
+.IP
+Mismatch score, default: \fB\-1\fR
+.HP
+\fB\-bg\fR, \fB\-\-barcode\-gap\fR NUM
+.IP
+Gap score, default: \fB\-7\fR
+.IP
+Adapter removal:
+.HP
+\fB\-a\fR, \fB\-\-adapters\fR FILE
+.IP
+Fasta file with adapters, or
+barcodes to remove within
+reads
+.HP
+\fB\-as\fR, \fB\-\-adapter\-seq\fR STR
+.IP
+Single adapter sequence as
+alternative to adapters
+option
+.HP
+\fB\-ae\fR, \fB\-\-adapter\-trim\-end\fR STR
+.IP
+Type of alignment for
+removal, see section
+trim\-end modes, default:
+RIGHT
+.HP
+\fB\-an\fR, \fB\-\-adapter\-tail\-length\fR NUM
+.IP
+Number of bases for tail
+trim\-end types, default:
+adapter length
+.HP
+\fB\-ao\fR, \fB\-\-adapter\-min\-overlap\fR NUM
+.IP
+Minimum overlap of adapter
+and read, default: 1
+.HP
+\fB\-at\fR, \fB\-\-adapter\-threshold\fR NUM
+.IP
+Allowed mismatches and
+indels per 10 bases for
+adapter, default: 3.0
+.HP
+\fB\-am\fR, \fB\-\-adapter\-match\fR NUM
+.IP
+Match score, default: 1
+.HP
+\fB\-ai\fR, \fB\-\-adapter\-mismatch\fR NUM
+.IP
+Mismatch score, default: \fB\-1\fR
+.HP
+\fB\-ag\fR, \fB\-\-adapter\-gap\fR NUM
+.IP
+Gap score, default: \fB\-7\fR
+.IP
+Filtering and trimming:
+.HP
+\fB\-u\fR, \fB\-\-max\-uncalled\fR NUM
+.IP
+Allowed uncalled bases (N or
+\&.) in reads, default: 0
+.HP
+\fB\-x\fR, \fB\-\-pre\-trim\-left\fR NUM
+.IP
+Trim specified number of
+bases on 5' end of reads
+before detection
+.HP
+\fB\-y\fR, \fB\-\-pre\-trim\-right\fR NUM
+.IP
+Trim specified number of
+bases on 3' end of reads
+before detection
+.HP
+\fB\-q\fR, \fB\-\-pre\-trim\-phred\fR NUM
+.IP
+Trim 3' end until specified
+or higher quality reached,
+precise fastq format
+.HP
+\fB\-z\fR, \fB\-\-post\-trim\-length\fR NUM
+.IP
+Trim to specified read
+length from 3' end after
+removal
+.HP
+\fB\-m\fR, \fB\-\-min\-readlength\fR NUM
+.IP
+Minimum read length to
+remain after removal,
+default: 18
+.IP
+Logging and tagging:
+.HP
+\fB\-l\fR, \fB\-\-log\-level\fR STR
+.IP
+Print alignments for all or
+modified reads. One of ALL,
+MOD, and TAB
+.HP
+\fB\-s\fR, \fB\-\-single\-reads\fR
+.IP
+Output single reads of
+patially too short paired
+reads
+.HP
+\fB\-d\fR, \fB\-\-length\-dist\fR
+.IP
+Write length distribution
+for read output files
+.HP
+\fB\-o\fR, \fB\-\-fasta\-output\fR
+.IP
+Prefer non\-quality formats
+fasta and csfasta for output
+.HP
+\fB\-e\fR, \fB\-\-number\-tags\fR
+.IP
+Replace read tags by
+ascending number to save
+space
+.HP
+\fB\-g\fR, \fB\-\-removal\-tags\fR
+.IP
+Tag reads that are subject
+to adapter or barcode
+removal
+.IP
+Trim\-end modes:
+.IP
+ANY: longer part of read remains
+LEFT: align <= read end, right
+part remains
+RIGHT: align >= read start, left
+part remains
+LEFT_TAIL: consider first n bases
+of reads in alignment
+RIGHT_TAIL: use only last n bases,
+see tail\-length options
+.PP
+.SH EXAMPLES
+.IP
+flexbar \fB\-t\fR target \fB\-f\fR fastq\-i1.3 \fB\-r\fR
+reads.fastq \fB\-b\fR bar.fasta \fB\-a\fR
+adap.fasta
+.IP
+flexbar \fB\-t\fR target \fB\-f\fR csfastq \fB\-r\fR
+reads.csfastq \fB\-a\fR adapters.fasta
+\fB\-ae\fR LEFT
+.PP
+Further documentation on: flexbar.sourceforge.net

Added: trunk/packages/flexbar/trunk/debian/manpages
===================================================================
--- trunk/packages/flexbar/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/flexbar/trunk/debian/manpages	2013-02-23 11:34:50 UTC (rev 13068)
@@ -0,0 +1 @@
+debian/*.1

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