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Merge pull request #81 from hasindu2008/master 

minimap2 on ARM processors
This commit is contained in:
Heng Li 2017-12-16 09:40:41 -05:00 committed by GitHub
parent ab345e600b 8995e2e078
commit 23a846c594
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3 changed files with 1712 additions and 0 deletions
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17
Makefile
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@ -6,11 +6,17 @@ PROG= minimap2
PROG_EXTRA= sdust minimap2-lite PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread LIBS= -lm -lz -lpthread
ifeq ($(arm_neon),)
ifeq ($(sse2only),) ifeq ($(sse2only),)
OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
else else
OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
endif endif
else
OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
INCLUDES+=-I sse2neon
endif
.SUFFIXES:.c .o .SUFFIXES:.c .o
@ -53,6 +59,17 @@ ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
ksw2_dispatch.o:ksw2_dispatch.c ksw2.h ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
clean: clean:
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg* rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*

6
README.md
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@ -359,7 +359,13 @@ In general, minimap2 is a young project with most code written since June, 2017.
It may have bugs and room for improvements. Bug reports and suggestions are It may have bugs and room for improvements. Bug reports and suggestions are
warmly welcomed. warmly welcomed.
## <a name="arm"></a>Compiling for ARM with NEON
* Minimap2 can be compiled for ARM processors having NEON SIMD support. Compile as
```
make arm_neon=1
```
[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
[sam]: https://samtools.github.io/hts-specs/SAMv1.pdf [sam]: https://samtools.github.io/hts-specs/SAMv1.pdf

1689
sse2neon/emmintrin.h 100644
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