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

--- a/Makefile
+++ b/Makefile
@@ -115,7 +115,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
 SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
 
 # TABIX = tabixpp/tabix.o
-FASTAHACK = fastahack/Fasta.o
 SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
 REPEATS = smithwaterman/Repeats.o
 INDELALLELE = smithwaterman/IndelAllele.o
@@ -124,9 +123,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
 FSOM = fsom/fsom.o
 FILEVERCMP = filevercmp/filevercmp.o
 
-INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
-LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
-
+INCLUDES = `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -I$(INC_DIR)
+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
 
 all: $(OBJECTS) $(BINS)
 
@@ -179,9 +177,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
 
 $(INDELALLELE): $(SMITHWATERMAN)
 
-$(FASTAHACK): pre
-	cd fastahack && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
-
 #$(FSOM):
 #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
 
@@ -196,11 +191,11 @@ $(FILEVERCMP): pre
 $(SHORTBINS): pre
 	$(MAKE) bin/$@
 
-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
+$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(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) pre
-	ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
+libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
+	ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
 	cp libvcflib.a $(LIB_DIR)
 
 
@@ -229,6 +224,6 @@ clean:
 	rm -rf $(OBJ_DIR)
 	# cd tabixpp && make clean
 	# cd smithwaterman && make clean
-	cd fastahack && make clean
+	# cd fastahack && make clean
 
 .PHONY: clean all test pre