The following commit has been merged in the master branch:
commit fa026f0479f1ce52255c6f25dba299b7de54d5f6
Author: Shaun Jackman sjack...@debian.org
Date: Wed Dec 7 13:21:47 2011 -0800
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 758ddfb..3809c40 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+gmap (2011-11-30-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman sjack...@debian.org Wed, 07 Dec 2011 10:46:12 -0800
+
gmap (2011-10-16-1) unstable; urgency=low
* New upstream release.
diff --git a/debian/gmap.1 b/debian/gmap.1
index 6958409..37a581a 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -1,4 +1,4 @@
-.TH GMAP 1 August 2011 GMAP 2011-08-15 User Commands
+.TH GMAP 1 Nov 2011 GMAP 2011-11-30 User Commands
.SH NAME
gmap \- Genomic Mapping and Alignment Program
.SH SYNOPSIS
@@ -84,7 +84,8 @@ Max total intron length (default 240)
Amount of unaligned sequence that triggers
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.
+with some non-chimeric reads. To turn off, set to
+a large value (greater than the query length).
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR
Number of worker threads
@@ -175,6 +176,11 @@ prints two paths if chimera detected, else one.
If more than maximum number of paths are found, then nothing is
printed.
.TP
+\fB--suboptimal-score\fR=\fIINT\fR
+Report only paths whose score is within this value of the
+best path. By default, if this option is not provided,
+the program prints all paths found.
+.TP
\fB\-O\fR, \fB\-\-ordered\fR
Print output in same order as input (relevant
only if there is more than one worker thread)
@@ -226,10 +232,6 @@ Options for SAM output
\fB\-\-no\-sam\-headers\fR
Do not print headers beginning with '@'
.TP
-\fB\-\-noncanonical\-splices\fR=\fISTRING\fR
-Print non-canonical genomic gaps greater than 20 nt
-in CIGAR string as STRING. Allowed values: N (default), D.
-.TP
\fB\-\-read\-group\-id\fR=\fISTRING\fR
Value to put into read-group id (RG-ID) field
.TP
diff --git a/debian/gmap_setup.1 b/debian/gmap_setup.1
index 8338d17..aab9a93 100644
--- a/debian/gmap_setup.1
+++ b/debian/gmap_setup.1
@@ -1,4 +1,4 @@
-.TH GMAP_SETUP 1 Aug 2010 GMAP 2010-07-27 User Commands
+.TH GMAP_SETUP 1 Nov 2011 GMAP 2011-11-30 User Commands
.SH NAME
gmap_setup \- create a genome database for GMAP or GSNAP
.SH SYNOPSIS
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index a70434b..ca9500b 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -1,4 +1,4 @@
-.TH GSNAP 1 August 2011 GMAP 2011-08-15 User Commands
+.TH GSNAP 1 Nov 2011 GMAP 2011-11-30 User Commands
.SH NAME
gsnap \- Genomic Short-read Nucleotide Alignment Program
.SH SYNOPSIS
@@ -104,8 +104,14 @@ Whether to count unknown (N) characters in the genome as a
mismatch
.TP
\fB--terminal-threshold\fR=\fIINT\fR
Threshold for searching for a terminal alignment (from one end of the
-read to the best possible position at the other end) (default 3).
-To turn off terminal alignments, set this to a high value.
+read to the best possible position at the other end) (default 2).
+For example, if this value is 2, then if GSNAP finds an exact or
+1-mismatch alignment, it will not try to find a terminal alignment.
+Note that this default value may not be low enough if you want to
+obtain terminal alignments for very short reads, although such reads
+probably don't have enough specificity for terminal alignments anyway.
+To turn off terminal alignments, set this to a high value, greater
+than the value for --max-mismatches.
.TP
\fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
Penalty for an indel (default 2).
@@ -141,7 +147,13 @@ To turn off, use the value off.
.TP
\fB\-\-trim\-mismatch\-score\fR=\fIINT\fR
Score to use for mismatches when trimming at ends (default is -3;
-to turn off trimming, specify 0)
+to turn off trimming, specify 0). Warning: turning trimming off
+will give false positive mismatches at the ends of reads
+.TP
+\fB--trim-indel-score\fR=\fIINT\fR
+Score to use for indels when trimming at ends (default is -4;
+to turn off trimming, specify 0). Warning: turning trimming off
+will give false positive indels at the ends of reads
.TP
\fB\-V\fR, \fB\-\-snpsdir\fR=\fISTRING\fR
Directory for SNPs index files (created using snpindex) (default is
@@ -230,6 +242,12 @@ Look for splicing involving known sites or known introns
See README instructions for the distinction between known sites and
known introns
.TP
+\fB--ambig-splice-noclip\fR
+For ambiguous known splicing at ends of the read, do not clip at the
+splice site, but extend instead into the intron. This flag makes
+sense only if you provide the --use-splicing flag, and you are trying
+to eliminate all soft clipping with --trim-mismatch-score=0
+.TP
\fB\-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR
Definition of local novel splicing event (default 20)
