[Debian-med-packaging] [SCM] gmap branch, master, updated. upstream/2010-07-21-12-g11dc610

[Shaun Jackman]

The following commit has been merged in the master branch:
commit dbbce6c6fba20b3a13d87dbec7898f1e2db18338
Author: Shaun Jackman <sjackman at debian.org>
Date:   Thu Jul 22 11:57:07 2010 -0700

    * Update the man pages.

diff --git a/debian/gmap.1 b/debian/gmap.1
index 9eeea13..0da5261 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -1,4 +1,4 @@
-.TH GMAP "1" "April 2010" "GMAP 2010-03-09" "User Commands"
+.TH GMAP "1" "July 2010" "GMAP 2010-07-21" "User Commands"
 .SH NAME
 gmap \- Genomic Mapping and Alignment Program
 .SH SYNOPSIS
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 7d098a9..7ab6da9 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -42,6 +42,8 @@ defaults to the ultrafast level of ((readlength+2)/12 \- 2))
 If specified between 0.0 and 1.0, then treated as a fraction
 of each read length.  Otherwise, treated as an integral number
 of mismatches (including indel and splicing penalties)
+For RNA-Seq, you may need to increase this value to 10 or so,
+to align reads extending past the ends of an exon.
 .TP
 \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
 Penalty for an indel (default 1000, essentially turning it off).
@@ -77,8 +79,12 @@ on non\-unique or repetitive reads
  3 = greedy frequent: mask frequent oligomers first, then try no masking if alignments not found
  4 = greedy repetitive: mask frequent and repetitive oligomers first, then try no masking if alignments not found
 .TP
-\fB\-T\fR, \fB\-\-trim\fR=\fIINT\fR
-Trim mismatches at ends (0 = no (default), 1 = yes)
+\fB-a\fR, \fB--adapter-strip\fR=\fISTRING\fR
+Method for removing adapters from reads. Currently allowed values: paired
+.TP
+\fB\-T\fR, \fB\-\-trimlength\fR=\fIINT\fR
+Maximum amount of trimming of mismatches at ends (default is 1000;
+to turn off trimming, specify 0)
 .TP
 \fB\-2\fR, \fB\-\-dibase\fR
 Input is 2\-base encoded (e.g., SOLiD), with database built
@@ -113,7 +119,7 @@ within shortsplicedist (\fB\-w\fR flag) or with novelspliceprob (\fB\-x\fR flag)
 Definition of local novel splicing event (default 200000)
 .TP
 \fB\-e\fR, \fB\-\-local\-splice\-penalty\fR=\fIINT\fR
-Penalty for a local splice (default 2).
+Penalty for a local splice (default 0).
 Counts against mismatches allowed
 .TP
 \fB\-E\fR, \fB\-\-distant\-splice\-penalty\fR=\fIINT\fR

-- 
Align mRNA and EST sequences to a genome