[med-svn] [freebayes] 01/02: Adapt bamtools patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository freebayes.

commit e771b8c9b2dc7efb130f373a9db1f12b073cc20e
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 14:32:26 2016 +0200

    Adapt bamtools patch
---
 debian/patches/use_debian_packaged_bamtools.patch | 46 +++++++++++------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch
index 068db14..96cc2e6 100644
--- a/debian/patches/use_debian_packaged_bamtools.patch
+++ b/debian/patches/use_debian_packaged_bamtools.patch
@@ -2,10 +2,10 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Wed, 28 May 2014 21:23:38 +0200
 Description: Use Debian packaged bamtools
 
---- freebayes.orig/src/Makefile
-+++ freebayes/src/Makefile
-@@ -12,11 +12,10 @@
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,11 +12,10 @@ C=gcc
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
  #CFLAGS=-O3 -static -D VERBOSE_DEBUG  # enables verbose debugging via --debug2
  
 -BAMTOOLS_ROOT=../bamtools
@@ -18,7 +18,7 @@ Description: Use Debian packaged bamtools
  
  all: autoversion ../bin/freebayes ../bin/bamleftalign
  
-@@ -34,10 +33,6 @@
+@@ -34,10 +33,6 @@ gprof:
  
  .PHONY: all static debug profiling gprof
  
@@ -29,7 +29,7 @@ Description: Use Debian packaged bamtools
  
  OBJECTS=BedReader.o \
  		CNV.o \
-@@ -69,8 +64,7 @@
+@@ -70,8 +65,7 @@ OBJECTS=BedReader.o \
  		../vcflib/smithwaterman/LeftAlign.o \
  		../vcflib/smithwaterman/Repeats.o \
  		../vcflib/smithwaterman/IndelAllele.o \
@@ -39,48 +39,48 @@ Description: Use Debian packaged bamtools
  
  HEADERS=multichoose.h version_git.h
  
-@@ -85,10 +79,10 @@
+@@ -86,10 +80,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
  dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
- 	$(CC) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
+ 	$(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
  
 -bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
--	$(CC) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-+	$(CC) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
+-	$(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS)
++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o
++	$(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
  
 -bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS)
 +bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
- 	$(CC) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
+ 	$(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
  
  
-@@ -103,7 +97,7 @@
+@@ -104,7 +98,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
  dummy.o: dummy.cpp AlleleParser.o Allele.o
- 	$(CC) $(CFLAGS) $(INCLUDE) -c dummy.cpp
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
  
 -freebayes.o: freebayes.cpp TryCatch.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+freebayes.o: freebayes.cpp TryCatch.h 
- 	$(CC) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
++freebayes.o: freebayes.cpp TryCatch.h
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
  
  fastlz.o: fastlz.c fastlz.h
-@@ -124,7 +118,7 @@
+@@ -125,7 +119,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
  Ewens.o: Ewens.cpp Ewens.h
- 	$(CC) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
  
 -AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
 +AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
- 	$(CC) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
  
  Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -169,7 +163,7 @@
+@@ -173,7 +167,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
  bamfiltertech.o: bamfiltertech.cpp
- 	$(CC) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
  
 -LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a
 +LeftAlign.o: LeftAlign.h LeftAlign.cpp
- 	$(CC) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
  
  IndelAllele.o: IndelAllele.cpp IndelAllele.h
-@@ -259,6 +253,5 @@
+@@ -263,6 +257,5 @@ autoversion:
  
  clean:
  	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}

-- 
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