Changed sse2neon with SIMDe. Added building non-SIMD version.
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mbrcic
parent
29f67a1666
commit
9e6fdd376b
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@ -0,0 +1,3 @@
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[submodule "lib/simde"]
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path = lib/simde
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url = https://github.com/nemequ/simde.git
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31
Makefile
31
Makefile
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@ -1,11 +1,13 @@
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CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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CPPFLAGS= -DHAVE_KALLOC
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
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INCLUDES= -Ilib/simde/simde
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o
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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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ifeq ($(no_simd),) # if no_simd is not defined
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OBJS+=ksw2_ll_sse.o
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ifeq ($(arm_neon),) # if arm_neon is not defined
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ifeq ($(sse2only),) # if sse2only is not defined
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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@ -14,13 +16,15 @@ else # if sse2only is defined
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endif
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else # if arm_neon is defined
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OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
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INCLUDES+=-Isse2neon
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ifeq ($(aarch64),) #if aarch64 is not defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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else #if aarch64 is defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
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endif
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endif
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else
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OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o
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endif
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ifneq ($(asan),)
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CFLAGS+=-fsanitize=address
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@ -83,15 +87,28 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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# NEON-specific targets on ARM
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ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
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ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
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ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
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# no-SIMD version
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ksw2_ll_nosimd.o:ksw2_ll_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
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ksw2_extz2_nosimd.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
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ksw2_extd2_nosimd.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
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ksw2_exts2_nosimd.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
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# other non-file targets
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@ -4,14 +4,16 @@
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#include "ksw2.h"
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#ifdef __SSE2__
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#include <emmintrin.h>
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//#include <emmintrin.h>
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#include <x86/sse2.h>
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#ifdef KSW_SSE2_ONLY
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#undef __SSE4_1__
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#endif
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#ifdef __SSE4_1__
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#include <smmintrin.h>
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//#include <smmintrin.h>
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#include <x86/sse4.1.h>
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#endif
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#ifdef KSW_CPU_DISPATCH
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@ -4,14 +4,15 @@
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#include "ksw2.h"
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#ifdef __SSE2__
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#include <emmintrin.h>
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//#include <emmintrin.h>
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#include <x86/sse2.h>
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#ifdef KSW_SSE2_ONLY
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#undef __SSE4_1__
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#endif
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#ifdef __SSE4_1__
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#include <smmintrin.h>
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//#include <smmintrin.h>
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#include <x86/sse4.1.h>
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#endif
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#ifdef KSW_CPU_DISPATCH
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@ -3,14 +3,16 @@
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#include "ksw2.h"
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#ifdef __SSE2__
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#include <emmintrin.h>
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//#include <emmintrin.h>
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#include <x86/sse2.h>
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#ifdef KSW_SSE2_ONLY
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#undef __SSE4_1__
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#endif
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#ifdef __SSE4_1__
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#include <smmintrin.h>
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//#include <smmintrin.h>
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#include <x86/sse4.1.h>
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#endif
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#ifdef KSW_CPU_DISPATCH
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@ -1,7 +1,8 @@
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#include <stdlib.h>
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#include <stdint.h>
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#include <string.h>
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#include <emmintrin.h>
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//#include <emmintrin.h>
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#include <x86/sse2.h>
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#include "ksw2.h"
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#ifdef __GNUC__
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@ -0,0 +1 @@
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Subproject commit b30129b3b48a6823013da2b309c50a081177b6b8
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