[med-svn] [libvcflib] 05/07: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository libvcflib.

commit 136e5b57aa9509be84fe9e5c0a864b7e189fbdf8
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 20 10:01:54 2016 +0200

    Adapt patches
---
 debian/patches/use_debian_packaged_tabixpp.patch | 51 ++++++++----------------
 1 file changed, 16 insertions(+), 35 deletions(-)

diff --git a/debian/patches/use_debian_packaged_tabixpp.patch b/debian/patches/use_debian_packaged_tabixpp.patch
index 3e19ae6..a9167e0 100644
--- a/debian/patches/use_debian_packaged_tabixpp.patch
+++ b/debian/patches/use_debian_packaged_tabixpp.patch
@@ -1,47 +1,28 @@
 --- a/Makefile
 +++ b/Makefile
-@@ -80,7 +80,7 @@ BIN_SOURCES = src/vcfecho.cpp \
+@@ -114,7 +114,7 @@ BIN_SOURCES = src/vcfecho.cpp \
  BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  
 -TABIX = tabixpp/tabix.o
 +# TABIX = tabixpp/tabix.o
  FASTAHACK = fastahack/Fasta.o
- SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o 
+ SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  REPEATS = smithwaterman/Repeats.o
-@@ -90,7 +90,7 @@ LEFTALIGN = smithwaterman/LeftAlign.o
- FSOM = fsom/fsom.o
- FILEVERCMP = filevercmp/filevercmp.o
- 
--INCLUDES = -I. -Itabixpp/htslib/ -L. -Ltabixpp/ -Ltabixpp/htslib/
-+INCLUDES = -I. -Itabixpp/htslib/ #-L. -Ltabixpp/ -Ltabixpp/htslib/
- LDFLAGS = -lvcflib -ltabix -lhts -lpthread -lz -lm
- 
- 
-@@ -115,7 +115,7 @@ profiling:
- gprof:
- 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
- 
--$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX)
-+$(OBJECTS): $(SOURCES) $(HEADERS) # $(TABIX)
- 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
- 
- $(TABIX):
-@@ -147,8 +147,8 @@ $(SHORTBINS):
- $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP)
- 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
- 
--libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX)
--	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-+libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) # $(TABIX)
-+	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) # $(TABIX)
- 
- 
- test: $(BINS)
-@@ -158,7 +158,7 @@ clean:
- 	rm -f $(BINS) $(OBJECTS)
- 	rm -f ssw_cpp.o ssw.o
- 	rm -f libvcflib.a
+@@ -162,7 +162,8 @@ intervaltree: pre
+ 	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ $(TABIX): pre
+-	cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
++	echo "No need to create separately packaged tabixpp"
++	# cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ $(SMITHWATERMAN): pre
+ 	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
+@@ -218,7 +219,7 @@ clean:
+ 	rm -rf $(LIB_DIR)
+ 	rm -rf $(INC_DIR)
+ 	rm -rf $(OBJ_DIR)
 -	cd tabixpp && make clean
 +	# cd tabixpp && make clean
  	cd smithwaterman && make clean

-- 
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