Author: ajtravis-guest Date: 2013-04-25 09:33:47 +0000 (Thu, 25 Apr 2013) New Revision: 13414
Modified: trunk/packages/flexbar/trunk/debian/changelog trunk/packages/flexbar/trunk/debian/copyright trunk/packages/flexbar/trunk/debian/flexbar.1 Log: Updated for Flexbar v2.33 Modified: trunk/packages/flexbar/trunk/debian/changelog =================================================================== --- trunk/packages/flexbar/trunk/debian/changelog 2013-04-25 09:29:53 UTC (rev 13413) +++ trunk/packages/flexbar/trunk/debian/changelog 2013-04-25 09:33:47 UTC (rev 13414) @@ -1,5 +1,7 @@ -flexbar (2.32-1) unstable; urgency=low +flexbar (2.33-1) unstable; urgency=low + * Updated from new upstream sources + * Initial release (Closes: #701539) - -- Tony Travis <[email protected]> Sat, 23 Feb 2013 11:24:05 +0000 + -- Tony Travis <[email protected]> Mon, 22 Apr 2013 16:58:06 +0000 Modified: trunk/packages/flexbar/trunk/debian/copyright =================================================================== --- trunk/packages/flexbar/trunk/debian/copyright 2013-04-25 09:29:53 UTC (rev 13413) +++ trunk/packages/flexbar/trunk/debian/copyright 2013-04-25 09:33:47 UTC (rev 13414) @@ -29,18 +29,6 @@ On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". -Files: include/tbb/* -Copyright: Copyright (c) 2005-2011 Intel Corporation -License: GPLv2_runtime_exception - This program makes use of the TBB (Threading Building Blocks) library. - see <http://threadingbuildingblocks.org/>. Specifically, the TBB open-source - license is the same license used by the GNU libstdc++ library in gcc 4.2.1 - (and earlier). - . - For a complete description of the TBB license, please visit the official GNU - website for GPLv2 and the runtime exception. - <http://www.gnu.org/licenses/old-licenses/gpl-2.0.html> - Files: include/seqan/* Copyright: © 2007-2010 Andreas Döring <[email protected]> Modified: trunk/packages/flexbar/trunk/debian/flexbar.1 =================================================================== --- trunk/packages/flexbar/trunk/debian/flexbar.1 2013-04-25 09:29:53 UTC (rev 13413) +++ trunk/packages/flexbar/trunk/debian/flexbar.1 2013-04-25 09:33:47 UTC (rev 13414) @@ -1,47 +1,51 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. -.TH FLEXBAR "1" "February 2013" "flexbar version 2.32" "User Commands" +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4. +.TH FLEXBAR "1" "April 2013" "flexbar " "User Commands" .SH NAME -flexbar \- flexible barcode and adapter removal for sequencing platforms -.SH SYNOPSIS +flexbar \- manual page for flexbar +.SH DESCRIPTION +flexbar \- flexible barcode and adapter removal +.PP +SYNOPSIS .IP flexbar \fB\-t\fR target \fB\-f\fR format \fB\-r\fR reads [\-b barcodes] [\-a adapters] [options] .PP -.SH OPTIONS +DESCRIPTION .HP \fB\-h\fR, \fB\-\-help\fR .IP -Display this help message +Displays this help message. .HP -\fB\-v\fR, \fB\-\-version\fR +\fB\-\-version\fR .IP -Display program version +Display version information .HP \fB\-c\fR, \fB\-\-cite\fR .IP -View citation information +Shows citation information. .IP Basic options: .HP \fB\-n\fR, \fB\-\-threads\fR NUM .IP -Number of threads, default: -1 +Number of threads. Default: +1. .HP \fB\-t\fR, \fB\-\-target\fR STR .IP -Prefix for output file names +Prefix for output file +names. .HP \fB\-r\fR, \fB\-\-reads\fR FILE .IP Input file with reads, that -may contain barcodes +may contain barcodes. .HP \fB\-p\fR, \fB\-\-reads2\fR FILE .IP Second input file for paired -read scenario +read scenario. .HP \fB\-f\fR, \fB\-\-format\fR STR .IP @@ -50,7 +54,7 @@ fastq, fastq\-sanger, fastq\-solexa, fastq\-i1.3, fastq\-i1.5, fastq\-i1.8 -(illumina 1.8+) +(illumina 1.8+). .IP Barcode detection: .HP @@ -58,60 +62,57 @@ .IP Fasta file with barcodes, specify (br) to use separate -barcode reads +barcode reads. .HP \fB\-br\fR, \fB\-\-barcode\-reads\fR FILE .IP Fasta or fastq file with separate barcode reads, if -not within reads +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 +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 +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 +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 +barcode. Default: 1.0. .HP \fB\-bk\fR, \fB\-\-barcode\-keep\fR .IP Keep barcodes within reads -instead of removal +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 +Alignment match score. +Default: 1. .HP \fB\-bi\fR, \fB\-\-barcode\-mismatch\fR NUM .IP -Mismatch score, default: \fB\-1\fR +Alignment mismatch score. +Default: \fB\-1\fR. .HP \fB\-bg\fR, \fB\-\-barcode\-gap\fR NUM .IP -Gap score, default: \fB\-7\fR +Alignment gap score. +Default: \fB\-7\fR. .IP Adapter removal: .HP @@ -119,123 +120,130 @@ .IP Fasta file with adapters, or barcodes to remove within -reads +reads. .HP \fB\-as\fR, \fB\-\-adapter\-seq\fR STR .IP Single adapter sequence as alternative to adapters -option +option. .HP \fB\-ae\fR, \fB\-\-adapter\-trim\-end\fR STR .IP -Type of alignment for -removal, see section -trim\-end modes, default: -RIGHT +Type of adapter 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 +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 +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 +adapter. Default: 3.0. .HP \fB\-am\fR, \fB\-\-adapter\-match\fR NUM .IP -Match score, default: 1 +Alignment match score. +Default: 1. .HP \fB\-ai\fR, \fB\-\-adapter\-mismatch\fR NUM .IP -Mismatch score, default: \fB\-1\fR +Alignment mismatch score. +Default: \fB\-1\fR. .HP \fB\-ag\fR, \fB\-\-adapter\-gap\fR NUM .IP -Gap score, default: \fB\-7\fR +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 +\&.) 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 +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 +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 +or higher quality reached. .HP \fB\-z\fR, \fB\-\-post\-trim\-length\fR NUM .IP Trim to specified read length from 3' end after -removal +removal. .HP \fB\-m\fR, \fB\-\-min\-readlength\fR NUM .IP Minimum read length to -remain after removal, -default: 18 +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 +Print valid sequence +alignments of 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 +Output single reads for +partially 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 +fasta and csfasta for +output. .HP +\fB\-i\fR, \fB\-\-length\-dist\fR +.IP +Write length distribution +for read output files. +.HP \fB\-e\fR, \fB\-\-number\-tags\fR .IP Replace read tags by ascending number to save -space +space. .HP \fB\-g\fR, \fB\-\-removal\-tags\fR .IP Tag reads that are subject to adapter or barcode -removal +removal. +.HP +\fB\-d\fR, \fB\-\-random\-tags\fR .IP +Random read tags at barcode +or adapter positions with N. +.IP Trim\-end modes: .IP ANY: longer part of read remains @@ -248,14 +256,32 @@ RIGHT_TAIL: use only last n bases, see tail\-length options .PP -.SH EXAMPLES +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 +VERSION +.IP +flexbar version: 2.33 +Last update March 18, 2013 +.PP Further documentation on: flexbar.sourceforge.net +.PP +flexbar version 2.33 +.SH "SEE ALSO" +The full documentation for +.B flexbar +is maintained as a Texinfo manual. If the +.B info +and +.B flexbar +programs are properly installed at your site, the command +.IP +.B info flexbar +.PP +should give you access to the complete manual. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
