[med-svn] r16553 - in trunk/packages/staden-io-lib/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-04-02 06:31:32 +0000 (Wed, 02 Apr 2014)
New Revision: 16553

Added:
   trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch
Modified:
   trunk/packages/staden-io-lib/trunk/debian/changelog
   trunk/packages/staden-io-lib/trunk/debian/patches/series
Log:
Commit NMU with patch from upstream Aleksandar Zlicic


Modified: trunk/packages/staden-io-lib/trunk/debian/changelog
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/changelog	2014-04-01 07:48:51 UTC (rev 16552)
+++ trunk/packages/staden-io-lib/trunk/debian/changelog	2014-04-02 06:31:32 UTC (rev 16553)
@@ -1,3 +1,13 @@
+staden-io-lib (1.13.5-1.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix io_lib/bam.c read
+    Patch by Aleksandar Zlicic
+    Add fix-bam-read.patch
+    Closes: #736565
+
+ -- Anibal Monsalve Salazar <anibal at debian.org>  Tue, 01 Apr 2014 04:19:52 +0100
+
 staden-io-lib (1.13.5-1) unstable; urgency=medium
 
   * New upstream release. 

Added: trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch	2014-04-02 06:31:32 UTC (rev 16553)
@@ -0,0 +1,36 @@
+Date: Mon, 31 Mar 2014 19:22:13 +0200
+From: Aleksandar Zlicic <Aleksandar.Zlicic at imgtec.com>
+Subject: staden-io-lib: fix io_lib/bam.c read
+
+https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565
+
+We have fixed a bug reported for the staden-io-lib package
+(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565).  The cause
+of this problem is an error in function bam_get_seq(), or to be more
+precise, function's implementation for non-intel architectures.
+
+Function bam_get_seq is used for reading data from alignment blocks in
+BAM files, block by block.
+
+In special cases, when the alignment block being read is the last
+block in BAM file, and the block has no cigar operations and segment
+sequence stored inside of it, function incorrectly detects
+end-of-file.
+
+In that case, block has actually been successfully read, but because
+of erroneous end-of-file detection, it isn't written to output file in
+SAM format.
+
+Attached patch fixes this issue.
+
+--- a/io_lib/bam.c	2014-01-07 17:01:12.000000000 +0000
++++ bio_lib//bam.c	2014-04-01 04:05:16.762660873 +0100
+@@ -1635,7 +1635,7 @@ int bam_get_seq(bam_file_t *b, bam_seq_t
+ 
+     /* The remainder, word aligned */
+     blk_size = blk_ret;
+-    if ((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0)
++    if (((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0) && blk_size != 0)
+ 	return 0;
+     if (blk_size+4 != blk_ret) {
+ 	if (blk_size != blk_ret) {

Modified: trunk/packages/staden-io-lib/trunk/debian/patches/series
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/series	2014-04-01 07:48:51 UTC (rev 16552)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/series	2014-04-02 06:31:32 UTC (rev 16553)
@@ -1 +1,2 @@
 pathmax.patch
+fix-bam-read.patch