[med-svn] r19027 - in trunk/packages/rna-star/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-04-04 08:35:53 +0000 (Sat, 04 Apr 2015)
New Revision: 19027

Modified:
   trunk/packages/rna-star/trunk/debian/changelog
   trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
   trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
Log:
New upstream version (adapted patches)


Modified: trunk/packages/rna-star/trunk/debian/changelog
===================================================================
--- trunk/packages/rna-star/trunk/debian/changelog	2015-04-04 06:50:23 UTC (rev 19026)
+++ trunk/packages/rna-star/trunk/debian/changelog	2015-04-04 08:35:53 UTC (rev 19027)
@@ -1,8 +1,8 @@
 rna-star (2.4.0k-1) UNRELEASED; urgency=medium
 
-  * New upstream version
+  * New upstream version (adapted patches)
 
- -- Andreas Tille <tille at debian.org>  Sat, 04 Apr 2015 08:49:22 +0200
+ -- Andreas Tille <tille at debian.org>  Sat, 04 Apr 2015 10:35:14 +0200
 
 rna-star (2.4.0i-1) unstable; urgency=low
 

Modified: trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-04-04 06:50:23 UTC (rev 19026)
+++ trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-04-04 08:35:53 UTC (rev 19027)
@@ -56,9 +56,9 @@
  
 --- a/source/STAR.cpp
 +++ b/source/STAR.cpp
-@@ -314,7 +314,7 @@ int main(int argInN, char* argIn[]) {
+@@ -331,7 +331,7 @@ int main(int argInN, char* argIn[]) {
          vector <string> bamBinNamesV;
-         for (uint32 ibin=0; ibin<RAchunk[0]->chunkOutBAMcoord->nBins; ibin++) {
+         for (uint32 ibin=0; ibin<nBins; ibin++) {
              
 -            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin));            
 +            bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+std::to_string((uint) ibin));            

Modified: trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-04-04 06:50:23 UTC (rev 19026)
+++ trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-04-04 08:35:53 UTC (rev 19027)
@@ -49,7 +49,7 @@
  
 --- a/source/STAR.cpp
 +++ b/source/STAR.cpp
-@@ -22,7 +22,7 @@
+@@ -23,7 +23,7 @@
  #include "mapThreadsSpawn.h"
  #include "ErrorWarning.h"
  
@@ -100,6 +100,6 @@
  //external libs
 -#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
 +#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
+ #define SAMTOOLS_SAM_H  "htslib/htslib/sam.h"
  
  using namespace std;
-