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--- 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.
|
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