Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 23 Jun 2016 09:10:54 +0200
Description: Use Debian packaged libtabixpp

--- a/Makefile
+++ b/Makefile
@@ -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
 REPEATS = smithwaterman/Repeats.o
@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
 FSOM = fsom/fsom.o
 FILEVERCMP = filevercmp/filevercmp.o
 
-INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
+INCLUDES = -I$(INC_DIR)
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
 
 
 all: $(OBJECTS) $(BINS)
@@ -152,7 +152,7 @@ profiling:
 gprof:
 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
 
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 multichoose: pre
@@ -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)/
@@ -190,8 +191,8 @@ $(SHORTBINS): pre
 $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
 
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
+libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
+	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
 	cp libvcflib.a $(LIB_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
 	cd fastahack && make clean