[med-svn] r17220 - trunk/packages/staden-io-lib/trunk/debian/patches

[Charles Plessy]

Author: plessy
Date: 2014-06-18 22:28:07 +0000 (Wed, 18 Jun 2014)
New Revision: 17220

Removed:
   trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch
Modified:
   trunk/packages/staden-io-lib/trunk/debian/patches/series
Log:
Removed debian/patches/fix-bam-read.patch, applied upstream.


Deleted: trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch	2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch	2014-06-18 22:28:07 UTC (rev 17220)
@@ -1,36 +0,0 @@
-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	2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/series	2014-06-18 22:28:07 UTC (rev 17220)
@@ -1,2 +1 @@
 pathmax.patch
-fix-bam-read.patch