diff bwa-0.6.2/Makefile @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/Makefile	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,49 @@
+CC=			gcc
+CXX=		g++
+CFLAGS=		-g -Wall -O2
+CXXFLAGS=	$(CFLAGS)
+AR=			ar
+DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
+LOBJS=		bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \
+			bwaseqio.o bwase.o kstring.o
+AOBJS=		QSufSort.o bwt_gen.o \
+			is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
+			bwape.o cs2nt.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=	.
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+.cc.o:
+		$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+bwa:libbwa.a $(AOBJS) main.o
+		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+
+libbwa.a:$(LOBJS)
+		$(AR) -csru $@ $(LOBJS)
+
+bwa.o:bwa.h
+
+QSufSort.o:QSufSort.h
+
+bwt.o:bwt.h
+bwtio.o:bwt.h
+bwtaln.o:bwt.h bwtaln.h kseq.h
+bntseq.o:bntseq.h
+bwtgap.o:bwtgap.h bwtaln.h bwt.h
+
+bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
+bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
+bwtsw2_main.o:bwtsw2.h
+
+clean:
+		rm -f gmon.out *.o a.out $(PROG) *~ *.a