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separate out spliced alignment; not right yet

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Heng Li
2017-08-12 18:54:32 -04:00
parent 53b3265d84
commit 61eef0575c
5 changed files with 332 additions and 28 deletions
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Makefile
+2 -4
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@@ -2,7 +2,7 @@ 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_extd2_noins_sse.o ksw2_ll_sse.o \
OBJS= kthread.o kalloc.o ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_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
@@ -33,9 +33,6 @@ 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*
@@ -53,6 +50,7 @@ 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_extd2_sse.o: ksw2.h kalloc.h
ksw2_exts2_sse.o: ksw2.h kalloc.h
ksw2_extz2_sse.o: ksw2.h kalloc.h
ksw2_ll_sse.o: ksw2.h kalloc.h
main.o: bseq.h minimap.h mmpriv.h