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r159: use two-piece gap penalty

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This commit is contained in:
Heng Li
2017-07-08 10:26:00 -04:00
parent 9823317e8f
commit cc554aee43
9 changed files with 499 additions and 113 deletions
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Makefile
+7 -10
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@@ -1,17 +1,13 @@
CC= gcc
CFLAGS= -g -Wall -O2 -Wc++-compat
CFLAGS= -g -Wall -O2 -Wc++-compat -march=native
CPPFLAGS= -DHAVE_KALLOC
INCLUDES= -I.
OBJS= kthread.o kalloc.o ksw2_extz2_sse.o misc.o bseq.o sketch.o sdust.o \
index.o chain.o align.o hit.o map.o format.o
OBJS= kthread.o kalloc.o ksw2_extz2_sse.o ksw2_extd2_sse.o misc.o bseq.o \
sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o
PROG= minimap2
PROG_EXTRA= sdust
LIBS= -lm -lz -lpthread
ifneq ($(sse4),)
CFLAGS += -msse4
endif
.SUFFIXES:.c .o
.c.o:
@@ -34,18 +30,19 @@ 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)
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
# DO NOT DELETE
align.o: minimap.h mmpriv.h bseq.h ksw2.h
align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
bseq.o: bseq.h kseq.h
chain.o: minimap.h mmpriv.h bseq.h kalloc.h
format.o: mmpriv.h minimap.h bseq.h
hit.o: mmpriv.h minimap.h bseq.h kalloc.h
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
kalloc.o: kalloc.h
ksw2_extz2_sse.o: ksw2.h
ksw2_extd2_sse.o: ksw2.h kalloc.h
ksw2_extz2_sse.o: ksw2.h kalloc.h
main.o: bseq.h minimap.h mmpriv.h
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
misc.o: minimap.h ksort.h