The following commit has been merged in the master branch:
commit e21796d88ba8cf78ddbb3c851e412329ee96b25b
Author: Shaun Jackman sjack...@debian.org
Date: Tue Aug 23 14:54:38 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 9cb0e8c..c3c12ac 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+gmap (2011-08-15-1) unstable; urgency=low
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.2.
+
+ -- Shaun Jackman sjack...@debian.org Tue, 23 Aug 2011 10:45:46 -0700
+
gmap (2011-03-11-1) unstable; urgency=low
* New upstream release.
diff --git a/debian/control b/debian/control
index 12fa327..c11fbfd 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team
debian-med-packaging@lists.alioth.debian.
DM-Upload-Allowed: yes
Uploaders: Shaun Jackman sjack...@debian.org
Build-Depends: debhelper (= 7.0.50~), autotools-dev
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
Homepage: http://research-pub.gene.com/gmap/
Vcs-Git: git://git.debian.org/git/debian-med/gmap.git
Vcs-Browser: http://git.debian.org/?p=debian-med/gmap.git
diff --git a/debian/copyright b/debian/copyright
index 23f323b..465e2a2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -3,7 +3,7 @@ Name: GMAP
Maintainer: Thomas Wu t...@gene.com, Colin K. Watanabe c...@gene.com
Source: http://research-pub.gene.com/gmap/
-Copyright: 2005 Genentech, Inc.
+Copyright: 2011 Genentech, Inc.
License: other
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
@@ -43,7 +43,7 @@ License: LGPL-2.1+
See `/usr/share/common-licenses/LGPL'.
Files: debian/*
-Copyright: 2010 Shaun Jackman sjack...@debian.org
+Copyright: 2011 Shaun Jackman sjack...@debian.org
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
diff --git a/debian/gmap.1 b/debian/gmap.1
index aa488f0..6a89b8e 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -1,4 +1,4 @@
-.TH GMAP 1 Mar 2011 GMAP 2011-03-11 User Commands
+.TH GMAP 1 August 2011 GMAP 2011-08-15 User Commands
.SH NAME
gmap \- Genomic Mapping and Alignment Program
.SH SYNOPSIS
@@ -18,6 +18,11 @@ Genome directory
Genome database. If argument is '?' (with
the quotes), this command lists available databases.
.TP
+\fB-k\fR, \fB--kmer\fR=\fIINT\fR
+kmer size to use in genome database (allowed values: 12-15). If not
+specified, the program will find the highest available kmer size in
+the genome database
+.TP
\fB\-G\fR, \fB\-\-genomefull\fR
Use full genome (all ASCII chars allowed;
built explicitly during setup), not
@@ -44,28 +49,32 @@ Computation options
2 allocate mmap preload mmap preload (default)
3 allocate allocatemmap preload
4 allocate allocateallocate
+ 5 expandallocateallocate
Note: For a single sequence, all data structures use mmap.
-If mmap not available and allocate not chosen, then will use fileio (slow)
+If mmap not available and allocate not chosen, then will use fileio
+(very slow)
+.TP
+\fB-K\fR, \fB--intronlength\fR=\fIINT\fR
+Max length for one internal intron (default 100)
.TP
-\fB\-K\fR, \fB\-\-intronlength\fR=\fIINT\fR
-Max length for one intron (default 100)
+\fB-w\fR, \fB--localsplicedist\fR=\fIINT\fR
+Max length for known splice sites at ends of sequence (default 20)
.TP
\fB\-L\fR, \fB\-\-totallength\fR=\fIINT\fR
Max total intron length (default 240)
.TP
\fB\-x\fR, \fB\-\-chimera-margin\fR=\fIINT\fR
Amount of unaligned sequence that triggers
-search for a chimera (default off)
+search for the remaining sequence (default 40).
+Enables alignment of chimeric reads, and may help
+with some non-chimeric reads. To turn off, set to 0.
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR
Number of worker threads
.TP
-\fB\-s\fR, \fB\-\-altstrain\fR
-Search alternate strains in addition
-.TP
\fB\-C\fR, \fB\-\-chrsubsetfile\fR=\fIfilename\fR
-User\-suppled chromosome subset file
+User\-supplied chromosome subset file
.TP
\fB\-c\fR, \fB\-\-chrsubset\fR=\fIstring\fR
Chromosome subset to search
@@ -78,11 +87,19 @@ sense_filter, antisense_filter, or auto (default))
Trim end exons with fewer than given number of matches
(in nt, default 12)
.TP
-\fB\-X\fR, \fB\-\-canonical\fR=\fIINT\fR
-Reward for canonical and semi\-canonical introns
+\fB--cross-species\fR
+For cross-species alignments, use a more sensitive search for
+canonical splicing
+.TP
+\fB--canonical-mode\fR=\fIINT\fR
+Reward for canonical and semi-canonical introns
0=low reward, 1=high reward (default), 2=low reward for
high\-identity sequences and high reward otherwise
.TP
+\fB--allow-close-indels\fR=\fIINT\fR
+Allow an insertion and deletion close to each other
+(0=no, 1=yes (default), 2=only for high-quality
