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r281: don't open long gaps on query

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Heng Li
2017-08-10 15:04:59 -04:00
parent c59b0781bc
commit 163fa36ee6
5 changed files with 41 additions and 13 deletions
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9
Makefile
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@@ -2,8 +2,8 @@ CC= gcc
CFLAGS= -g -Wall -O2 -Wc++-compat
CPPFLAGS= -DHAVE_KALLOC
INCLUDES= -I.
OBJS= kthread.o kalloc.o ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_ll_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 ksw2_extd2_noins_sse.o ksw2_ll_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 minimap2-lite
LIBS= -lm -lz -lpthread
@@ -33,6 +33,9 @@ libminimap2.a:$(OBJS)
sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
ksw2_extd2_noins_sse.o:ksw2_extd2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_NO_LONG_INS $(INCLUDES) $< -o $@
clean:
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
@@ -45,7 +48,7 @@ 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
example.o: minimap.h kseq.h
format.o: mmpriv.h minimap.h bseq.h
format.o: kalloc.h 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