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--- bwa-0.7.13/Makefile
+++ bwa-0.7.13/Makefile
@@ -1,8 +1,8 @@
-CC= gcc
+CC?= gcc
#CC= clang --analyze
-CFLAGS= -g -Wall -Wno-unused-function -O2
+CFLAGS?= -g -Wall -Wno-unused-function -O2
WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
-AR= ar
+AR?= ar
DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
@@ -26,10 +26,10 @@
all:$(PROG)
bwa:libbwa.a $(AOBJS) main.o
- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
bwamem-lite:libbwa.a example.o
- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
libbwa.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
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