[med-svn] [SCM] gmap branch, master, updated. upstream/2011-10-16-29-gfa026f0

[Shaun Jackman]

The following commit has been merged in the master branch:
commit fa026f0479f1ce52255c6f25dba299b7de54d5f6
Author: Shaun Jackman <sjackman at 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 <sjackman at 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 2400000)
 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 200000)
 .TP
@@ -259,6 +277,11 @@ Penalty for antistranded splicing when using stranded RNA-Seq
 protocols. A positive value, such as 1, expects antisense on the
 first read and sense on the second read. Default is 0, which treats
 sense and antisense equally well
+.TP
+\fB--merge-distant-samechr\fR
+Report distant splices on the same chromosome as a single splice, if possible.
+Will produce a single SAM line instead of two SAM lines, which is also done
+for translocations, inversions, and scramble events
 .SS
 Options for paired\-end reads
 .TP
@@ -270,6 +293,14 @@ without splicing (default 1000).  Used if -N or -s is not specified.
 Max total genomic length for RNA-Seq paired reads, or other reads
 that could have a splice (default 200000). Used if -N or -s is specified.
 Should probably match the value for -w, --localsplicedist.
+.TP
+\fB--pairexpect\fR=\fIINT\fR
+Expected paired-end length, used for calling splices in medial part of
+paired-end reads (default 200)
+.TP
+\fB--pairdev\fR=\fIINT\fR
+Allowable deviation from expected paired-end length, used for
+calling splices in medial part of paired-end reads (default 25)
 .SS
 Options for quality scores
 .TP
@@ -292,11 +323,6 @@ FASTQ quality scores are zero at this ASCII value
 Shift FASTQ quality scores by this amount in output
 (default is 0 for sanger protocol; to change Illumina input
 to Sanger output, select -31)
-.TP
-\fB--mapq-unique-score\fR=\fIINT\fR
-For multiple results, consider as a unique result if only one of the
-results has a MAPQ score equal or greater than this (if not selected,
-then reports all multiple results, up to npaths)
 .SS
 Output options
 .TP

-- 
Align mRNA and EST sequences to a genome