Update Makefile

Makefile

@@ -1,40 +1,37 @@
-
 # HAPCUT2 MAKEFILE
 default: all
 
-CFLAGS=-Wall -g -O3 -Wall -D_GNU_SOURCE
+CFLAGS=-Wall -g -O3 -Wall -D_GNU_SOURCE -I/home/jialechen/software/htslib-1.20/include
+LDFLAGS=-L/home/jialechen/software/htslib-1.20/lib -lhts
 
 # DIRECTORIES
 B=build
 H=hairs-src
 X=hapcut2-src
-HTSLIB=htslib #/usr/common/src/htslib #path/to/htslib/
+HTSLIB=/home/jialechen/software/htslib-1.20
 T=test
 # below is the path to CUnit directory, change if need be
 CUNIT=/usr/include/CUnit
-LDFLAGS=-L$(HTSLIB)
 
 all: $(B)/extractHAIRS $(B)/HAPCUT2
 
-#temporarily removed -O2 flag after -I$(HTSLIB)
 $(B)/extractHAIRS: $(B)/bamread.o $(B)/hashtable.o $(B)/readvariant.o $(B)/readfasta.o $(B)/hapfragments.o $(H)/extracthairs.c $(H)/parsebamread.c $(H)/realignbamread.c $(H)/nw.c $(H)/realign_pairHMM.c $(H)/estimate_hmm_params.c | $(B)
-	$(CC) $(CFLAGS) $(LDFLAGS) -I$(HTSLIB) -g $(B)/bamread.o $(B)/hapfragments.o $(B)/hashtable.o $(B)/readfasta.o $(B)/readvariant.o -o $(B)/extractHAIRS $(H)/extracthairs.c -pthread -lhts -lm -lz -lcurl -llzma -lbz2
-#temporarily removed -O2 flag after -I$(HTSLIB)
+	$(CC) $(CFLAGS) $(LDFLAGS) -g $(B)/bamread.o $(B)/hapfragments.o $(B)/hashtable.o $(B)/readfasta.o $(B)/readvariant.o -o $(B)/extractHAIRS $(H)/extracthairs.c -pthread -lm -lz -lcurl -llzma -lbz2
 
 $(B)/hapfragments.o: $(H)/hapfragments.c $(H)/hapfragments.h $(H)/readvariant.h | $(B)
 	$(CC) -c $(CFLAGS) $(H)/hapfragments.c -o $(B)/hapfragments.o
 
 $(B)/readvariant.o: $(H)/readvariant.c $(H)/readvariant.h $(H)/hashtable.h $(H)/hashtable.c | $(B)
-	$(CC) -c $(CFLAGS) -I$(HTSLIB) $(H)/readvariant.c -o $(B)/readvariant.o
+	$(CC) -c $(CFLAGS) $(H)/readvariant.c -o $(B)/readvariant.o
 
 $(B)/bamread.o: $(H)/bamread.h $(H)/bamread.c $(H)/readfasta.h $(H)/readfasta.c | $(B)
-	$(CC) -c $(CFLAGS) -I$(HTSLIB) $(H)/bamread.c -lhts -o $(B)/bamread.o
+	$(CC) -c $(CFLAGS) $(H)/bamread.c -o $(B)/bamread.o
 
 $(B)/hashtable.o: $(H)/hashtable.h $(H)/hashtable.c | $(B)
 	$(CC) -c $(CFLAGS) $(H)/hashtable.c -o $(B)/hashtable.o
 
 $(B)/readfasta.o: $(H)/readfasta.c $(H)/readfasta.h | $(B)
-	$(CC) -c $(CFLAGS) -I$(HTSLIB) $(H)/readfasta.c -o $(B)/readfasta.o
+	$(CC) -c $(CFLAGS) $(H)/readfasta.c -o $(B)/readfasta.o
 
 # BUILD HAPCUT2
 
@@ -78,7 +75,6 @@ install-hapcut2:
 install-hairs:
 	cp $(B)/extractHAIRS /usr/local/bin
 
-
 # UNINSTALL
 uninstall: uninstall-hapcut2 uninstall-hairs
 
@@ -88,7 +84,6 @@ uninstall-hapcut2:
 uninstall-hairs:
 	rm /usr/local/bin/extractHAIRS
 
-
 # CLEANUP
 clean:
 	rm -rf $(B)