[med-svn] r2733 - trunk/packages/ssake/trunk/debian

[tille at alioth.debian.org]

Author: tille
Date: 2008-11-24 15:18:18 +0000 (Mon, 24 Nov 2008)
New Revision: 2733

Added:
   trunk/packages/ssake/trunk/debian/tqs.1
Modified:
   trunk/packages/ssake/trunk/debian/ssake.1
   trunk/packages/ssake/trunk/debian/ssake.manpages
Log:
Man page for tqs


Modified: trunk/packages/ssake/trunk/debian/ssake.1
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake.1	2008-11-24 14:31:06 UTC (rev 2732)
+++ trunk/packages/ssake/trunk/debian/ssake.1	2008-11-24 15:18:18 UTC (rev 2733)
@@ -42,7 +42,7 @@
 Fasta file containing unpaired sequence reads (optional)
 
 .SH SEE ALSO
-/usr/share/doc/ssake/SSAKE.readmee between pairing reads are used interchangeably
+/usr/share/doc/ssake/SSAKE.readmee between
 
 .SH "AUTHORS"
 .PP

Modified: trunk/packages/ssake/trunk/debian/ssake.manpages
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake.manpages	2008-11-24 14:31:06 UTC (rev 2732)
+++ trunk/packages/ssake/trunk/debian/ssake.manpages	2008-11-24 15:18:18 UTC (rev 2733)
@@ -1 +1 @@
-debian/ssake.1
+debian/*.1

Added: trunk/packages/ssake/trunk/debian/tqs.1
===================================================================
--- trunk/packages/ssake/trunk/debian/tqs.1	                        (rev 0)
+++ trunk/packages/ssake/trunk/debian/tqs.1	2008-11-24 15:18:18 UTC (rev 2733)
@@ -0,0 +1,42 @@
+.TH "TQS" "1" "January 2008"
+.SH "NAME"
+tqs \- Trim Quality Solexa-Illumina Sequences
+
+.SH SYNOPSIS
+Quality trim solexa-Illumina sequence reads using user-defined thresholds.
+
+.SH "OPTIONS"
+.PP
+.IP "\-h, \-\-help                         " 10
+show this help message and exit
+.IP "\-f SEQFILE, \-\-sequence file=SEQFILE" 10
+Illumina sequence file - Output format from the 1G Genome Analyzer (_seq.txt):
+    7       1       255     669
+    AACCCCCACTCCTACAACGCCATCATTCCCCTCGAC
+.IP "\-q QUALFILE, \-\-qual file=QUALFILE  " 10
+A prb file containing all the Illumina intensities, as outputted by the 1G Genome Analyzer (_prb.txt)
+.IP "\-l MER, \-\-length=MER               " 10
+Length of sequence reads (i.e. Number of sequencing cycles, default=36)
+.IP "\-t THRESHOLD, \-\-threshold=THRESHOLD" 10
+Base intensity threshold value (-40 to 40, default=5)
+.IP "\-d DIFF, \-\-difference=DIFF         " 10
+Base intensity difference between top intensity and second best (1 to 80, default=5)
+.IP "\-c CONSEC, \-\-consec=CONSEC         " 10
+Minimum number of consecutive bases passing threshold values (default=20)
+.IP "\-v, \-\-verbose                      " 10
+Runs in Verbose mode.
+                                                                        
+.SH SEE ALSO
+/usr/share/doc/ssake/TQS.readmee
+
+.SH "AUTHORS"
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others).  Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.