index can be compiled; not tested yet

Makefile

@@ -0,0 +1,41 @@
+CC=			gcc
+CFLAGS=		-g -Wall -O2 -Wc++-compat -Wno-unused-function
+CPPFLAGS=
+INCLUDES=	-I.
+OBJS=		kalloc.o kthread.o bseq.o sketch.o sdust.o index.o
+PROG=		minimap2
+PROG_EXTRA=	sdust
+LIBS=		-lm -lz -lpthread
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+extra:all $(PROG_EXTRA)
+
+minimap2:libminimap2.a
+		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+
+libminimap2.a:$(OBJS)
+		$(AR) -csru $@ $(OBJS)
+
+sdust:sdust.c kalloc.o kdq.h kvec.h kseq.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+
+clean:
+		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
+
+depend:
+		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)
+
+# DO NOT DELETE
+
+bseq.o: bseq.h kseq.h
+index.o: kthread.h bseq.h minimap.h kvec.h kalloc.h khash.h
+kalloc.o: kalloc.h
+misc.o: minimap.h ksort.h
+sdust.o: kalloc.h kdq.h kvec.h sdust.h
+sketch.o: kvec.h kalloc.h minimap.h