[med-svn] r15932 - trunk/packages/flexbar/trunk/debian

Fri Jan 31 12:58:35 UTC 2014

Author: tille
Date: 2014-01-31 12:58:35 +0000 (Fri, 31 Jan 2014)
New Revision: 15932

Modified:
   trunk/packages/flexbar/trunk/debian/changelog
   trunk/packages/flexbar/trunk/debian/flexbar.1
Log:
Update manpage to new upstream version


Modified: trunk/packages/flexbar/trunk/debian/changelog
===================================================================

--- trunk/packages/flexbar/trunk/debian/changelog	2014-01-31 12:52:32 UTC (rev 15931)
+++ trunk/packages/flexbar/trunk/debian/changelog	2014-01-31 12:58:35 UTC (rev 15932)
@@ -9,6 +9,7 @@
      - cme fix dpkg-control
   * Build against Debian packaged seqan
   * debian/README.source: convinience copy of seqan removed by upstream
+  * debian/flexbar.1: Update manpage to new upstream version
 
  -- Andreas Tille <tille at debian.org>  Fri, 31 Jan 2014 12:55:18 +0100
 

Modified: trunk/packages/flexbar/trunk/debian/flexbar.1
===================================================================
--- trunk/packages/flexbar/trunk/debian/flexbar.1	2014-01-31 12:52:32 UTC (rev 15931)
+++ trunk/packages/flexbar/trunk/debian/flexbar.1	2014-01-31 12:58:35 UTC (rev 15932)
@@ -1,11 +1,8 @@
-.TH FLEXBAR "1" "April 2013" "2.33" "User Commands"
+.TH FLEXBAR "1" "January 2014" "2.4" "User Commands"
 .SH NAME
 flexbar \- flexible barcode and adapter removal for sequencing platforms
 .SH SYNOPSIS
-.B flexbar
-\fB\-t\fR target \fB\-f\fR format \fB\-r\fR
-reads [\-b barcodes] [\-a adapters]
-[options]
+flexbar \fB\-r\fR reads [\-t target] [\-b barcodes] [\-a adapters] [options]
 .SH DESCRIPTION
 Flexbar preprocesses high-throughput sequencing data efficiently. It
 demultiplexes barcoded runs and removes adapter sequences. Moreover,
@@ -23,255 +20,156 @@
 .IP
 Displays this help message.
 .HP
-\fB\-\-version\fR
+\fB\-w\fR, \fB\-\-advanced\fR
 .IP
-Display version information
+Print advanced options help screen.
 .HP
-\fB\-c\fR, \fB\-\-cite\fR
+\fB\-i\fR, \fB\-\-cite\fR
 .IP
-Shows citation information.
+Show program reference for citation.
 .IP
 Basic options:
 .HP
 \fB\-n\fR, \fB\-\-threads\fR NUM
 .IP
-Number of threads. Default:
-1.
+Number of threads to employ. Default: 1.
 .HP
 \fB\-t\fR, \fB\-\-target\fR STR
 .IP
-Prefix for output file
-names.
+Prefix for output file names or paths. Default: flexbar.
 .HP
 \fB\-r\fR, \fB\-\-reads\fR FILE
 .IP
-Input file with reads, that
-may contain barcodes.
+Fasta/q file or stdin (\-) with reads that may contain barcodes.
 .HP
 \fB\-p\fR, \fB\-\-reads2\fR FILE
 .IP
-Second input file for paired
-read scenario.
+Second input file of paired reads, gz and bz2 files supported.
 .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+).
+Quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+).
+.HP
+\fB\-c\fR, \fB\-\-color\-space\fR
 .IP
+Input in color\-space format csfasta or csfastq in sanger scaling.
+.IP
 Barcode detection:
 .HP
 \fB\-b\fR, \fB\-\-barcodes\fR FILE
 .IP
-Fasta file with barcodes,
-specify (br) to use separate
-barcode reads.
+Fasta file with barcodes for demultiplexing that may contain N.
 .HP
 \fB\-br\fR, \fB\-\-barcode\-reads\fR FILE
 .IP
-Fasta or fastq file with
-separate barcode reads, if
-not within reads.
+Fasta/q file composed of separate barcode reads for detection.
 .HP
 \fB\-be\fR, \fB\-\-barcode\-trim\-end\fR STR
 .IP
-Type of barcoding within
-reads, see section trim\-end
-modes. Default: ANY.
+Type of detection, 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 modes. Default:
-barcode length.
-.HP
 \fB\-bo\fR, \fB\-\-barcode\-min\-overlap\fR NUM
 .IP
-Minimum overlap of barcode
-and read. Default: barcode
-length.
+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.
+Allowed mismatches and gaps per 10 bases overlap. Default: 1.0.
 .HP
-\fB\-bk\fR, \fB\-\-barcode\-keep\fR
+\fB\-bu\fR, \fB\-\-barcode\-unassigned\fR
 .IP
-Keep barcodes within reads
-instead of removal.
-.HP
-\fB\-bm\fR, \fB\-\-barcode\-match\fR NUM
+Include unassigned reads in output generation.
 .IP
-Alignment match score.
-Default: 1.
-.HP
-\fB\-bi\fR, \fB\-\-barcode\-mismatch\fR NUM
-.IP
-Alignment mismatch score.
-Default: \fB\-1\fR.
-.HP
-\fB\-bg\fR, \fB\-\-barcode\-gap\fR NUM
-.IP
-Alignment 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.
+Fasta file with adapters for removal that may contain N.
 .HP
 \fB\-as\fR, \fB\-\-adapter\-seq\fR STR
 .IP
-Single adapter sequence as
-alternative to adapters
-option.
+Single adapter sequence as alternative to adapters option.
 .HP
 \fB\-ae\fR, \fB\-\-adapter\-trim\-end\fR STR
 .IP
-Type of adapter removal, see
-section trim\-end modes.
-Default: RIGHT.
+Type of 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 modes. Default:
-adapter length.
-.HP
 \fB\-ao\fR, \fB\-\-adapter\-min\-overlap\fR NUM
 .IP
-Minimum overlap of adapter
-and read. Default: 1.
+Minimum overlap of adapter and read sequence. 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
+Allowed mismatches and gaps per 10 bases overlap. Default: 3.0.
 .IP
-Alignment match score.
-Default: 1.
-.HP
-\fB\-ai\fR, \fB\-\-adapter\-mismatch\fR NUM
-.IP
-Alignment mismatch score.
-Default: \fB\-1\fR.
-.HP
-\fB\-ag\fR, \fB\-\-adapter\-gap\fR NUM
-.IP
-Alignment 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.
+Allowed uncalled bases (N or .) for each read. 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.
+Trim given number of bases on 5' read end 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.
+Trim specified number of bases on 3' end prior to detection.
 .HP
 \fB\-q\fR, \fB\-\-pre\-trim\-phred\fR NUM
 .IP
-Trim 3' end until specified
-or higher quality reached.
+Trim 3' end until specified or higher quality reached.
 .HP
-\fB\-z\fR, \fB\-\-post\-trim\-length\fR NUM
+\fB\-k\fR, \fB\-\-post\-trim\-length\fR NUM
 .IP
-Trim to specified read
-length from 3' end after
-removal.
+Trim to specified read length from 3' end after removal.
 .HP
-\fB\-m\fR, \fB\-\-min\-readlength\fR NUM
+\fB\-m\fR, \fB\-\-min\-read\-length\fR NUM
 .IP
-Minimum read length to
-remain after removal.
-Default: 18.
+Minimum read length to remain after removal. Default: 18.
 .IP
-Logging and tagging:
+Output selection:
 .HP
-\fB\-l\fR, \fB\-\-log\-level\fR STR
+\fB\-o\fR, \fB\-\-fasta\-output\fR
 .IP
-Print valid sequence
-alignments of reads. One of
-ALL, MOD, and TAB.
+Prefer non\-quality formats fasta and csfasta for output.
 .HP
-\fB\-s\fR, \fB\-\-single\-reads\fR
+\fB\-z\fR, \fB\-\-zip\-output\fR STR
 .IP
-Output single reads for
-partially too short paired
-reads.
+Enable direct compression of output files. One of GZ and BZ2.
 .HP
-\fB\-o\fR, \fB\-\-fasta\-output\fR
+\fB\-s\fR, \fB\-\-single\-reads\fR
 .IP
-Prefer non\-quality formats
-fasta and csfasta for
-output.
-.HP
-\fB\-i\fR, \fB\-\-length\-dist\fR
+Write single paired reads for too short counterparts.
 .IP
-Write length distribution
-for read output files.
+Logging and tagging:
 .HP
-\fB\-e\fR, \fB\-\-number\-tags\fR
+\fB\-l\fR, \fB\-\-log\-level\fR STR
 .IP
-Replace read tags by
-ascending number to save
-space.
+Print valid optimal read alignment. One of ALL, MOD, and TAB.
 .HP
 \fB\-g\fR, \fB\-\-removal\-tags\fR
 .IP
-Tag reads that are subject
-to adapter or barcode
-removal.
-.HP
-\fB\-d\fR, \fB\-\-random\-tags\fR
+Tag reads that are subject to adapter or barcode removal.
 .IP
-Random read tags at barcode
-or adapter positions with N.
-.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
+ANY: longer side of read remains after removal of overlap
+LEFT: right side remains after removal, align <= read end
+RIGHT: left part remains after removal, align >= read start
+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
-flexbar \fB\-t\fR target \fB\-f\fR csfastq \fB\-r\fR
-reads.csfastq \fB\-a\fR adapters.fasta
-\fB\-ae\fR LEFT
-.SH "SEE ALSO"
-Further documentation on: http://flexbar.sourceforge.net
-.SH AUTHOR
-This manual page was initially created using help2man(1) for version
-2.33 and enhanced by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
+flexbar \fB\-r\fR reads.fq \fB\-f\fR i1.8 \fB\-t\fR target \fB\-b\fR brc.fa \fB\-a\fR adap.fa
+flexbar \fB\-r\fR reads.csfastq.gz \fB\-a\fR adap.fa \fB\-ao\fR 5 \fB\-ae\fR LEFT \fB\-c\fR
+.PP
+.SH VERSION
+.IP
+flexbar version: 2.4
+Last update July 29, 2013
+.PP
+Advanced options: flexbar \fB\-w\fR
+.PP
+flexbar version 2.4


