[med-svn] [rna-star] 04/05: Adjusted patches for 2.5.1

Steffen Möller moeller at moszumanska.debian.org
Tue Feb 23 18:15:38 UTC 2016 

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moeller pushed a commit to branch master
in repository rna-star.

commit 8b3467af27a6436089584a7f4a36fe4144165bb6
Author: Steffen Moeller <moeller at debian.org>
Date:   Tue Feb 23 18:09:00 2016 +0100

    Adjusted patches for 2.5.1
---
 debian/patches/compilationstuff.patch    | 52 ++++--------------
 debian/patches/donotuse_own_htslib.patch | 92 +++++++++++++++++++++++---------
 2 files changed, 77 insertions(+), 67 deletions(-)

diff --git a/debian/patches/compilationstuff.patch b/debian/patches/compilationstuff.patch
index 419927e..cbf80d4 100644
--- a/debian/patches/compilationstuff.patch
+++ b/debian/patches/compilationstuff.patch
@@ -2,9 +2,11 @@ Author: Steffen Moeller <moeller at debian.org>,
 Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
 Description: Setting some compile options, fix some gcc errors
 
---- a/source/Parameters.h
-+++ b/source/Parameters.h
-@@ -60,7 +60,7 @@ class Parameters {
+Index: rna-star/source/Parameters.h
+===================================================================
+--- rna-star.orig/source/Parameters.h
++++ rna-star/source/Parameters.h
+@@ -61,7 +61,7 @@ class Parameters {
          int readFilesIndex;
          uint32 readFilesN;
          vector <string> readFilesIn, readFilesInTmp;
@@ -13,8 +15,10 @@ Description: Setting some compile options, fix some gcc errors
          uint readNmates;
          string readMatesLengthsIn;
          vector <string> readFilesCommand;
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
+Index: rna-star/source/STAR.cpp
+===================================================================
+--- rna-star.orig/source/STAR.cpp
++++ rna-star/source/STAR.cpp
 @@ -386,7 +386,7 @@ int main(int argInN, char* argIn[]) {
          vector <string> bamBinNamesV;
          for (uint32 ibin=0; ibin<nBins; ibin++) {
@@ -24,42 +28,4 @@ Description: Setting some compile options, fix some gcc errors
              struct stat buffer;
              if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
                  bamBinNamesV.pop_back();
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
- CXX ?= g++
- 
- # pre-defined flags
--LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
--LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
-+LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic $(LDFLAGS_add)
-+LDFLAGS_static := -static -static-libgcc -pthread -lhts -lz
- LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
- LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
--LDFLAGS_gdb := $(LDFLAGS_shared)
-+LDFLAGS_gdb += $(LDFLAGS_shared)
- 
- COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
- 
--CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
--CXXFLAGS_main := -O3 $(CXXFLAGS_common)
--CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)
-+CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add)
-+CXXFLAGS_main += -O3 $(CXXFLAGS_common)
-+CXXFLAGS_gdb +=  -O0 -g $(CXXFLAGS_common)
- 
- CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
- 
-@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
- 
- 
- %.o : %.cpp
--	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
-+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(COMPTIMEPLACE) $<
- 
- %.o : %.c
--	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
-+	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(COMPTIMEPLACE) $<
- 
- all: STAR
  
diff --git a/debian/patches/donotuse_own_htslib.patch b/debian/patches/donotuse_own_htslib.patch
index 03edc44..f274ea7 100644
--- a/debian/patches/donotuse_own_htslib.patch
+++ b/debian/patches/donotuse_own_htslib.patch
@@ -2,18 +2,48 @@ Author: Steffen Moeller <moeller at debian.org>,
 Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
 Description: Use Debian packaged htslib
 
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -12,7 +12,7 @@ CXXFLAGSextra ?=
+Index: rna-star/source/Makefile
+===================================================================
+--- rna-star.orig/source/Makefile
++++ rna-star/source/Makefile
+@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
  CXX ?= g++
  
  # pre-defined flags
 -LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
-+LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic -lz -lrt
- LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
++LDFLAGS_shared := -pthread -Bstatic -lhts -Bdynamic $(LDFLAGS_add)
++LDFLAGS_static := -static -static-libgcc -pthread -lhts -lz
  LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
-@@ -68,20 +68,17 @@ clean:
+-LDFLAGS_gdb := $(LDFLAGS_shared)
++LDFLAGS_gdb += $(LDFLAGS_shared)
+ 
+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
+ 
+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)
++CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add)
++CXXFLAGS_main += -O3 $(CXXFLAGS_common)
++CXXFLAGS_gdb +=  -O0 -g $(CXXFLAGS_common)
+ 
+ CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
+ 
+@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
+ 
+ 
+ %.o : %.cpp
+-	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(COMPTIMEPLACE) $<
+ 
+ %.o : %.c
+-	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(COMPTIMEPLACE) $<
+ 
+ all: STAR
+ 
+@@ -68,12 +68,10 @@ clean:
  .PHONY: CLEAN
  CLEAN:
  	rm -f *.o STAR Depend.list
@@ -23,10 +53,10 @@ Description: Use Debian packaged htslib
  cleanRelease:
  	rm -f *.o Depend.list
 -	$(MAKE) -C htslib clean
--
  
- ifneq ($(MAKECMDGOALS),clean)
- ifneq ($(MAKECMDGOALS),cleanRelease)
+ .PHONY: install
+ install:
+@@ -84,7 +82,7 @@ ifneq ($(MAKECMDGOALS),cleanRelease)
  ifneq ($(MAKECMDGOALS),CLEAN)
  ifneq ($(MAKECMDGOALS),STARforMac)
  ifneq ($(MAKECMDGOALS),STARforMacGDB)
@@ -35,7 +65,7 @@ Description: Use Debian packaged htslib
  	echo $(SOURCES)
  	/bin/rm -f ./Depend.list
  	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -92,11 +89,6 @@ endif
+@@ -95,11 +93,6 @@ endif
  endif
  endif
  
@@ -47,8 +77,10 @@ Description: Use Debian packaged htslib
  parametersDefault.xxd: parametersDefault
  	xxd -i parametersDefault > parametersDefault.xxd
  
---- a/source/bamRemoveDuplicates.cpp
-+++ b/source/bamRemoveDuplicates.cpp
+Index: rna-star/source/bamRemoveDuplicates.cpp
+===================================================================
+--- rna-star.orig/source/bamRemoveDuplicates.cpp
++++ rna-star/source/bamRemoveDuplicates.cpp
 @@ -1,7 +1,7 @@
  #include <unordered_map>
  #include "bamRemoveDuplicates.h"
@@ -58,8 +90,10 @@ Description: Use Debian packaged htslib
  #include "IncludeDefine.h"
  #include SAMTOOLS_BGZF_H
  #include "ErrorWarning.h"
---- a/source/bam_cat.c
-+++ b/source/bam_cat.c
+Index: rna-star/source/bam_cat.c
+===================================================================
+--- rna-star.orig/source/bam_cat.c
++++ rna-star/source/bam_cat.c
 @@ -52,8 +52,8 @@ THE SOFTWARE.
  #include <stdlib.h>
  #include <unistd.h>
@@ -71,8 +105,10 @@ Description: Use Debian packaged htslib
  #include <cstring>
  
  #define BUF_SIZE 0x10000
---- a/source/signalFromBAM.h
-+++ b/source/signalFromBAM.h
+Index: rna-star/source/signalFromBAM.h
+===================================================================
+--- rna-star.orig/source/signalFromBAM.h
++++ rna-star/source/signalFromBAM.h
 @@ -1,6 +1,6 @@
  #ifndef CODE_signalFromBAM
  #define CODE_signalFromBAM
@@ -81,8 +117,10 @@ Description: Use Debian packaged htslib
  #include  <fstream>
  #include <string>
  #include "Stats.h"
---- a/source/IncludeDefine.h
-+++ b/source/IncludeDefine.h
+Index: rna-star/source/IncludeDefine.h
+===================================================================
+--- rna-star.orig/source/IncludeDefine.h
++++ rna-star/source/IncludeDefine.h
 @@ -28,8 +28,8 @@
  #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
  
@@ -94,8 +132,10 @@ Description: Use Debian packaged htslib
  
  using namespace std;
  
---- a/source/BAMfunctions.cpp
-+++ b/source/BAMfunctions.cpp
+Index: rna-star/source/BAMfunctions.cpp
+===================================================================
+--- rna-star.orig/source/BAMfunctions.cpp
++++ rna-star/source/BAMfunctions.cpp
 @@ -1,5 +1,5 @@
  #include "BAMfunctions.h"
 -#include "htslib/htslib/kstring.h"
@@ -103,8 +143,10 @@ Description: Use Debian packaged htslib
  
  string bam_cigarString (bam1_t *b) {//output CIGAR string
  //    kstring_t strK;
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
+Index: rna-star/source/STAR.cpp
+===================================================================
+--- rna-star.orig/source/STAR.cpp
++++ rna-star/source/STAR.cpp
 @@ -26,7 +26,7 @@
  #include "sjdbInsertJunctions.h"
  #include "bam_cat.h"
@@ -114,8 +156,10 @@ Description: Use Debian packaged htslib
  #include "parametersDefault.xxd"
  
  
---- a/source/bam_cat.h
-+++ b/source/bam_cat.h
+Index: rna-star/source/bam_cat.h
+===================================================================
+--- rna-star.orig/source/bam_cat.h
++++ rna-star/source/bam_cat.h
 @@ -1,7 +1,7 @@
  #ifndef CODE_bam_cat
  #define CODE_bam_cat

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