Imported from my local bwa repository, the master repository.

Makefile

@@ -0,0 +1,55 @@
+CC=			gcc
+CXX=		g++
+CFLAGS=		-g -Wall -O2
+CXXFLAGS=	$(CFLAGS)
+DFLAGS=		-DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
+OBJS=		utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
+			bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
+			bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
+			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
+			bwtsw2_chain.o bamlite.o
+PROG=		bwa
+INCLUDES=	
+LIBS=		-lm -lz -lpthread -Lbwt_gen -lbwtgen
+SUBDIRS=	. bwt_gen
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+.cc.o:
+		$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+lib:
+
+bwa:lib-recur $(OBJS) main.o
+		$(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
+
+bwt.o:bwt.h
+bwtio.o:bwt.h
+bwtaln.o:bwt.h bwtaln.h kseq.h
+bwt1away.o:bwt.h bwtaln.h
+bwt2fmv.o:bwt.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
+
+cleanlocal:
+		rm -f gmon.out *.o a.out $(PROG) *~ *.a
+
+clean:cleanlocal-recur