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

--- a/Makefile
+++ b/Makefile
@@ -128,8 +128,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
 FSOM = fsom/fsom.o
 FILEVERCMP = filevercmp/filevercmp.o
 
-INCLUDES = -I$(INC_DIR)
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp
+INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman`
 
 all: $(OBJECTS) $(BINS) scriptToBin
 
@@ -161,17 +161,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 multichoose: pre
-	cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+	echo "Source does not contain dir multichoose"
+	# cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 intervaltree: pre
-	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+	echo "Source does not contain dir intervaltree"
+	# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 $(TABIX): pre
 	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)/
+	echo "Source does not contain dir smithwaterman"
+	# cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
 
 $(DISORDER): $(SMITHWATERMAN)
 
@@ -197,7 +200,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
 
 libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
+	ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
 	cp libvcflib.a $(LIB_DIR)
 
 
@@ -225,7 +228,7 @@ clean:
 	rm -rf $(INC_DIR)
 	rm -rf $(OBJ_DIR)
 	# cd tabixpp && make clean
-	cd smithwaterman && make clean
+	# cd smithwaterman && make clean
 	cd fastahack && make clean
 
 .PHONY: clean all test pre