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Jeremiah Wala
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May 14, 2015
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| Original file line number | Diff line number | Diff line change |
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| CC= gcc | ||
| #CC= clang --analyze | ||
| CFLAGS= -g -Wall -Wno-unused-function -O2 | ||
| WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS | ||
| AR= ar | ||
| DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) | ||
| LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o | ||
| AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ | ||
| is.o bwtindex.o bwape.o kopen.o pemerge.o \ | ||
| bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \ | ||
| bwtsw2_chain.o fastmap.o bwtsw2_pair.o | ||
| PROG= bwa | ||
| INCLUDES= | ||
| LIBS= -lm -lz -lpthread | ||
| SUBDIRS= . | ||
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| ifeq ($(shell uname -s),Linux) | ||
| LIBS += -lrt | ||
| endif | ||
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| .SUFFIXES:.c .o .cc | ||
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| .c.o: | ||
| $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ | ||
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| ##all:$(PROG) | ||
| all:libbwa.a | ||
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| bwa:libbwa.a $(AOBJS) main.o | ||
| $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) | ||
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| bwamem-lite:libbwa.a example.o | ||
| $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) | ||
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| libbwa.a:$(LOBJS) | ||
| $(AR) -csru $@ $(LOBJS) | ||
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| clean: | ||
| rm -f gmon.out *.o a.out $(PROG) *~ *.a | ||
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| depend: | ||
| ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) | ||
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| # DO NOT DELETE THIS LINE -- make depend depends on it. | ||
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| QSufSort.o: QSufSort.h | ||
| bamlite.o: bamlite.h malloc_wrap.h | ||
| bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h | ||
| bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kseq.h | ||
| bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h | ||
| bwamem.o: ksort.h utils.h kbtree.h | ||
| bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h | ||
| bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h | ||
| bwamem_pair.o: utils.h ksw.h | ||
| bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h | ||
| bwape.o: ksw.h khash.h | ||
| bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h | ||
| bwase.o: bwa.h ksw.h | ||
| bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h | ||
| bwashm.o: bwa.h bntseq.h bwt.h | ||
| bwt.o: utils.h bwt.h kvec.h malloc_wrap.h | ||
| bwt_gen.o: QSufSort.h malloc_wrap.h | ||
| bwt_lite.o: bwt_lite.h malloc_wrap.h | ||
| bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h | ||
| bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h | ||
| bwtindex.o: bntseq.h bwt.h utils.h malloc_wrap.h | ||
| bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h | ||
| bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h | ||
| bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h | ||
| bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h | ||
| bwtsw2_core.o: khash.h ksort.h | ||
| bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h | ||
| bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h | ||
| bwtsw2_pair.o: malloc_wrap.h ksw.h | ||
| example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h | ||
| fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h | ||
| is.o: malloc_wrap.h | ||
| kopen.o: malloc_wrap.h | ||
| kstring.o: kstring.h malloc_wrap.h | ||
| ksw.o: ksw.h malloc_wrap.h | ||
| main.o: kstring.h malloc_wrap.h utils.h | ||
| malloc_wrap.o: malloc_wrap.h | ||
| pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h | ||
| utils.o: utils.h ksort.h malloc_wrap.h kseq.h | ||
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| EMPTY_AUTOMAKE_TARGETS = dvi pdf ps info html tags ctags | ||
| .PHONY: $(EMPTY_AUTOMAKE_TARGETS) | ||
| $(EMPTY_AUTOMAKE_TARGETS): |
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