[med-svn] [freebayes] 02/02: vcflib needs to be packaged separately

[Andreas Tille]

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tille pushed a commit to branch master
in repository freebayes.

commit fa300cb0ee18c9a1c80e1eb08f0e9d9feafd1326
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 14:36:53 2016 +0200

    vcflib needs to be packaged separately
---
 debian/patches/series                           |  1 +
 debian/patches/use_debian_packaged_vcflib.patch | 59 +++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 58f3dd9..c24532e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+use_debian_packaged_vcflib.patch
 use_debian_packaged_bamtools.patch
diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch
new file mode 100644
index 0000000..b58ee7d
--- /dev/null
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -0,0 +1,59 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 22 Jun 2016 14:36:13 +0200
+Description: vcflib needs to be packaged separately
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -15,8 +15,8 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ BAMTOOLS_ROOT=../bamtools
+ VCFLIB_ROOT=../vcflib
+ 
+-LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm
+-INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
++LIBS = -ltabix -lz -lm
++INCLUDE = -I../ttmath
+ 
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+ 
+@@ -62,16 +62,7 @@ OBJECTS=BedReader.o \
+ 		Bias.o \
+ 		Contamination.o \
+ 		NonCall.o \
+-		SegfaultHandler.o \
+-		../vcflib/tabixpp/tabix.o \
+-		../vcflib/tabixpp/bgzf.o \
+-		../vcflib/smithwaterman/SmithWatermanGotoh.o \
+-		../vcflib/smithwaterman/disorder.c \
+-		../vcflib/smithwaterman/LeftAlign.o \
+-		../vcflib/smithwaterman/Repeats.o \
+-		../vcflib/smithwaterman/IndelAllele.o \
+-		Variant.o \
+-		$(BAMTOOLS_ROOT)/lib/libbamtools.a
++		SegfaultHandler.o
+ 
+ HEADERS=multichoose.h version_git.h
+ 
+@@ -179,17 +170,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $
+ IndelAllele.o: IndelAllele.cpp IndelAllele.h
+ 	$(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
+ 
+-Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
+-	$(CXX) $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
+-
+-../vcflib/tabixpp/tabix.o: ../vcflib/tabixpp/tabix.hpp ../vcflib/tabixpp/tabix.cpp
+-../vcflib/tabixpp/bgzf.o: ../vcflib/tabixpp/bgzf.c ../vcflib/tabixpp/bgzf.h
+-	cd ../vcflib/tabixpp && $(MAKE)
+-
+-../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
+-	cd ../vcflib/smithwaterman && $(MAKE)
+-
+-
+ VERSION_FILE=./version_git.h
+ RELEASED_VERSION_FILE=./version_release.txt
+ 
+@@ -264,5 +244,4 @@ autoversion:
+ clean:
+ 	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
+ 	test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean)
+-	cd ../vcflib/smithwaterman && make clean
+ 

-- 
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