gentoo-overlay/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch

--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,7 @@
-CC=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS+=		-Wall -Wno-unused-function
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
-AR=			ar
-DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+CPPFLAGS+=		-DHAVE_PTHREAD $(WRAP_MALLOC)
 LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
 			QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
 AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
@@ -21,16 +19,13 @@
 
 .SUFFIXES:.c .o .cc
 
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
 all:$(PROG)
 
 bwa:libbwa.a $(AOBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
 
 bwamem-lite:libbwa.a example.o
-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
 
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
@@ -39,7 +34,7 @@
 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
 
 depend:
-	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
+	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c )
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.