[med-svn] r18627 - trunk/packages/rna-star/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2015-01-29 22:26:07 +0000 (Thu, 29 Jan 2015)
New Revision: 18627

Modified:
   trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
   trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
Log:
Refesh patches


Modified: trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-01-29 22:01:55 UTC (rev 18626)
+++ trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch	2015-01-29 22:26:07 UTC (rev 18627)
@@ -1,8 +1,6 @@
-Index: star-2.4.0i/source/Parameters.h
-===================================================================
---- star-2.4.0i.orig/source/Parameters.h
-+++ star-2.4.0i/source/Parameters.h
-@@ -54,7 +54,7 @@
+--- a/source/Parameters.h
++++ b/source/Parameters.h
+@@ -54,7 +54,7 @@ class Parameters {
          int readFilesIndex;
          uint32 readFilesN;
          vector <string> readFilesIn, readFilesInTmp;
@@ -11,11 +9,9 @@
          uint readNmates;
          string readMatesLengthsIn;
          vector <string> readFilesCommand;
-Index: star-2.4.0i/source/Makefile
-===================================================================
---- star-2.4.0i.orig/source/Makefile
-+++ star-2.4.0i/source/Makefile
-@@ -17,28 +17,28 @@
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -17,28 +17,28 @@ OBJECTS = PackedArray.o SuffixArrayFuns.
          bam_cat.o
  SOURCES := $(wildcard *.cpp) $(wildcard *.c)
  
@@ -54,11 +50,9 @@
  
  all: STAR
  
-Index: star-2.4.0i/source/STAR.cpp
-===================================================================
---- star-2.4.0i.orig/source/STAR.cpp
-+++ star-2.4.0i/source/STAR.cpp
-@@ -314,7 +314,7 @@
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -314,7 +314,7 @@ int main(int argInN, char* argIn[]) {
          vector <string> bamBinNamesV;
          for (uint32 ibin=0; ibin<RAchunk[0]->chunkOutBAMcoord->nBins; ibin++) {
              

Modified: trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-01-29 22:01:55 UTC (rev 18626)
+++ trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch	2015-01-29 22:26:07 UTC (rev 18627)
@@ -1,8 +1,6 @@
-Index: star-2.4.0i/source/Makefile
-===================================================================
---- star-2.4.0i.orig/source/Makefile
-+++ star-2.4.0i/source/Makefile
-@@ -17,7 +17,7 @@
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -17,7 +17,7 @@ OBJECTS = PackedArray.o SuffixArrayFuns.
          bam_cat.o
  SOURCES := $(wildcard *.cpp) $(wildcard *.c)
  
@@ -11,7 +9,7 @@
  LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
  LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
-@@ -49,20 +49,17 @@
+@@ -49,20 +49,17 @@ clean:
  .PHONY: CLEAN
  CLEAN:
  	rm -f *.o STAR Depend.list
@@ -33,7 +31,7 @@
  	echo $(SOURCES)
  	/bin/rm -f ./Depend.list
  	$(CXX) $(CCFLAGS_common) -MM $^ >> Depend.list
-@@ -73,11 +70,6 @@
+@@ -73,11 +70,6 @@ endif
  endif
  endif
  
@@ -45,10 +43,8 @@
  parametersDefault.xxd: parametersDefault
  	xxd -i parametersDefault > parametersDefault.xxd
  
-Index: star-2.4.0i/source/STAR.cpp
-===================================================================
---- star-2.4.0i.orig/source/STAR.cpp
-+++ star-2.4.0i/source/STAR.cpp
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
 @@ -22,7 +22,7 @@
  #include "mapThreadsSpawn.h"
  #include "ErrorWarning.h"
@@ -58,10 +54,8 @@
  extern int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
  
  int main(int argInN, char* argIn[]) {
-Index: star-2.4.0i/source/bamRemoveDuplicates.cpp
-===================================================================
---- star-2.4.0i.orig/source/bamRemoveDuplicates.cpp
-+++ star-2.4.0i/source/bamRemoveDuplicates.cpp
+--- a/source/bamRemoveDuplicates.cpp
++++ b/source/bamRemoveDuplicates.cpp
 @@ -1,7 +1,7 @@
  #include <unordered_map>
  #include "bamRemoveDuplicates.h"
@@ -71,11 +65,9 @@
  #include "IncludeDefine.h"
  #include SAMTOOLS_BGZF_H
  #include "ErrorWarning.h"
-Index: star-2.4.0i/source/bam_cat.c
-===================================================================
---- star-2.4.0i.orig/source/bam_cat.c
-+++ star-2.4.0i/source/bam_cat.c
-@@ -49,8 +49,8 @@
+--- a/source/bam_cat.c
++++ b/source/bam_cat.c
+@@ -49,8 +49,8 @@ THE SOFTWARE.
  #include <stdlib.h>
  #include <unistd.h>
  
@@ -86,10 +78,8 @@
  #include <cstring>
  
  #define BUF_SIZE 0x10000
-Index: star-2.4.0i/source/signalFromBAM.h
-===================================================================
---- star-2.4.0i.orig/source/signalFromBAM.h
-+++ star-2.4.0i/source/signalFromBAM.h
+--- a/source/signalFromBAM.h
++++ b/source/signalFromBAM.h
 @@ -1,6 +1,6 @@
  #ifndef CODE_signalFromBAM
  #define CODE_signalFromBAM