[Debian-med-packaging] [SCM] gmap branch, master, updated. upstream/2010-07-20-10-g22dc19d

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 22dc19d520c5bba25007140edd3e10a19c06688f
Author: Shaun Jackman <sjackman at debian.org>
Date:   Thu Jul 22 11:44:51 2010 -0700

    * New upstream release.
    * debian/patches/install-data-local: Refresh.
    * debian/gsnap.1: Add -j,--quality-shift.

diff --git a/debian/changelog b/debian/changelog
index 44d158e..1f35477 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+gmap (2010-07-21-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Thu, 22 Jul 2010 11:36:34 -0700
+
 gmap (2010-07-20-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 67c7e85..7d098a9 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -1,4 +1,4 @@
-.TH GSNAP "1" "April 2010" "GMAP 2010-03-09" "User Commands"
+.TH GSNAP "1" "July 2010" "GMAP 2010-07-21" "User Commands"
 .SH NAME
 gsnap \- Genomic Short-read Nucleotide Alignment Program
 .SH SYNOPSIS
@@ -164,6 +164,9 @@ Exclude printing of failed alignments
 \fB\-A\fR, \fB\-\-format\fR=\fISTRING\fR
 Another format type, other than default.
 Currently implemented: sam
+.TP
+\fB-j\fR, \fB--quality-shift\fR=\fIINT\fR
+Shift FASTQ quality scores by this amount in SAM output (default -31)
 .SS
 Help options
 .TP
diff --git a/debian/patches/install-data-local b/debian/patches/install-data-local
index 37a6f5e..ea8278b 100644
--- a/debian/patches/install-data-local
+++ b/debian/patches/install-data-local
@@ -1,8 +1,8 @@
 Description: Add DESTDIR to install-data-local
 
---- gmap-2010-03-09.orig/Makefile.in
-+++ gmap-2010-03-09/Makefile.in
-@@ -642,7 +642,7 @@ uninstall-am:
+--- gmap.orig/Makefile.in
++++ gmap/Makefile.in
+@@ -642,7 +642,7 @@
  
  
  install-data-local:

-- 
Align mRNA and EST sequences to a genome