100 lines
3.7 KiB
Makefile
100 lines
3.7 KiB
Makefile
CC= gcc
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CFLAGS= -g -Wall -Wno-unused-function -mavx2 -O2
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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SHOW_PERF= -DSHOW_PERF
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SHOW_DATA_PERF= #-DSHOW_DATA_PERF
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FILTER_FULL_MATCH= #-DFILTER_FULL_MATCH
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USE_MT_READ= -DUSE_MT_READ
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AR= ar
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) $(SHOW_PERF) $(SHOW_DATA_PERF) $(FILTER_FULL_MATCH) $(USE_MT_READ) -DUSE_AVX2 -DKSW_EQUAL
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LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
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QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o yarn.o
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AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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bwape.o kopen.o pemerge.o maxk.o ksw_align_avx2.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o profiling.o \
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fmt_idx.o ksw_extend2_avx2.o ksw_extend2_avx2_u8.o \
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debug.o ertindex.o ertseeding.o
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PROG= fastbwa
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INCLUDES=
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LIBS= -lm -lz -lpthread -ldl
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SUBDIRS= .
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JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a
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ifeq ($(shell uname -s),Linux)
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LIBS += -lrt
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endif
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.SUFFIXES:.c .o .cc
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $(CPPFLAGS) $< -o $@
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all:$(PROG)
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#bwa:libbwa.a $(AOBJS) main.o
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# $(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
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$(PROG):libbwa.a $(AOBJS) main.o
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$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) $(JE_MALLOC) main.o -o $@ -L. -lbwa $(LIBS)
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bwamem-lite:libbwa.a example.o
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$(CC) $(CFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
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libbwa.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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clean:
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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depend:
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( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) $(CPPFLAGS) -- *.c )
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# DO NOT DELETE THIS LINE -- make depend depends on it.
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QSufSort.o: QSufSort.h
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bamlite.o: bamlite.h malloc_wrap.h
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bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h
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bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kvec.h
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bwa.o: kseq.h
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bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
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bwamem.o: ksort.h utils.h kbtree.h
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bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h
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bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
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bwamem_pair.o: utils.h ksw.h
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bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
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bwape.o: ksw.h khash.h
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bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
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bwase.o: bwa.h ksw.h
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bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
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bwashm.o: bwa.h bntseq.h bwt.h
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bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
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bwt_gen.o: QSufSort.h malloc_wrap.h
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bwt_lite.o: bwt_lite.h malloc_wrap.h
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bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
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bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
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bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h
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bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
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bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
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bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
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bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
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bwtsw2_core.o: khash.h ksort.h
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bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
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bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
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bwtsw2_pair.o: malloc_wrap.h ksw.h
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example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
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fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
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is.o: malloc_wrap.h
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kopen.o: malloc_wrap.h
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kstring.o: kstring.h malloc_wrap.h
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ksw.o: ksw.h neon_sse.h scalar_sse.h malloc_wrap.h
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main.o: kstring.h malloc_wrap.h utils.h
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malloc_wrap.o: malloc_wrap.h
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maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h
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pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
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rle.o: rle.h
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rope.o: rle.h rope.h
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utils.o: utils.h ksort.h malloc_wrap.h kseq.h
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