Merge branch 'master' into short
This commit is contained in:
Heng Li
commit
0031158936
30
Makefile
30
Makefile
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@ -1,15 +1,16 @@
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CC= gcc
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CFLAGS= -g -Wall -O2 -Wc++-compat
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CPPFLAGS= -DHAVE_KALLOC
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INCLUDES= -I.
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OBJS= kthread.o kalloc.o ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o ksw2_ll_sse.o \
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misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o ksw2_ll_sse.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 ($(sse2only),)
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CFLAGS+=-msse4
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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else
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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.SUFFIXES:.c .o
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@ -33,6 +34,27 @@ libminimap2.a:$(OBJS)
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sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
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$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
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ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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clean:
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
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23
NEWS.md
23
NEWS.md
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@ -1,3 +1,26 @@
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Release 2.1.1-r341 (6 September 2017)
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-------------------------------------
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This is a maintenance release that is expected to output identical alignment to
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v2.1. Detailed changes include:
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* Support CPU dispatch. By default, minimap2 is compiled with both SSE2 and
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SSE4 based implementation of alignment and automatically chooses the right
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one at runtime. This avoids unexpected errors on older CPUs (#21).
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* Improved Windows support as is requested by Oxford Nanopore (#19). Minimap2
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now avoids variable-length stacked arrays, eliminates alloca(), ships with
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getopt_long() and provides timing functions implemented with Windows APIs.
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* Fixed a potential segmentation fault when specifying -k/-w/-H with
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multi-part index (#23).
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* Fixed two memory leaks in example.c
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(2.1.1: 6 September 2017, r341)
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Release 2.1-r311 (25 August 2017)
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---------------------------------
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1
ksw2.h
1
ksw2.h
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@ -169,5 +169,4 @@ static inline int ksw_apply_zdrop(ksw_extz_t *ez, int is_rot, int32_t H, int a,
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}
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return 0;
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}
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#endif
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@ -0,0 +1,97 @@
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#ifdef KSW_CPU_DISPATCH
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#include <stdlib.h>
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#include "ksw2.h"
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#define SIMD_SSE 0x1
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#define SIMD_SSE2 0x2
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#define SIMD_SSE3 0x4
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#define SIMD_SSSE3 0x8
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#define SIMD_SSE4_1 0x10
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#define SIMD_SSE4_2 0x20
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#define SIMD_AVX 0x40
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#define SIMD_AVX2 0x80
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#define SIMD_AVX512F 0x100
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#ifndef _MSC_VER
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// adapted from https://github.com/01org/linux-sgx/blob/master/common/inc/internal/linux/cpuid_gnu.h
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void __cpuidex(int cpuid[4], int func_id, int subfunc_id)
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{
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#if defined(__x86_64__)
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asm volatile ("cpuid"
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: "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
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: "0" (func_id), "2" (subfunc_id));
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#else // on 32bit, ebx can NOT be used as PIC code
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asm volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"
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: "=a" (cpuid[0]), "=r" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
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: "0" (func_id), "2" (subfunc_id));
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#endif
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}
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#endif
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int x86_simd(void)
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{
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int flag = 0, cpuid[4], max_id;
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__cpuidex(cpuid, 0, 0);
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max_id = cpuid[0];
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if (max_id == 0) return 0;
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__cpuidex(cpuid, 1, 0);
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if (cpuid[3]>>25&1) flag |= SIMD_SSE;
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if (cpuid[3]>>26&1) flag |= SIMD_SSE2;
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if (cpuid[2]>>0 &1) flag |= SIMD_SSE3;
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if (cpuid[2]>>9 &1) flag |= SIMD_SSSE3;
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if (cpuid[2]>>19&1) flag |= SIMD_SSE4_1;
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if (cpuid[2]>>20&1) flag |= SIMD_SSE4_2;
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if (cpuid[2]>>28&1) flag |= SIMD_AVX;
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if (max_id >= 7) {
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__cpuidex(cpuid, 7, 0);
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if (cpuid[1]>>5 &1) flag |= SIMD_AVX2;
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if (cpuid[1]>>16&1) flag |= SIMD_AVX512F;
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}
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return flag;
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}
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void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez)
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{
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extern void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez);
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extern void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez);
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unsigned simd;
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simd = x86_simd();
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if (simd & SIMD_SSE4_1)
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ksw_extz2_sse41(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, flag, ez);
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else if (simd & SIMD_SSE2)
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ksw_extz2_sse2(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, flag, ez);
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else abort();
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}
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void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez)
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{
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extern void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez);
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extern void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez);
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unsigned simd;
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simd = x86_simd();
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if (simd & SIMD_SSE4_1)
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ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
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else if (simd & SIMD_SSE2)
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ksw_extd2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, flag, ez);
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else abort();
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}
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void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
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{
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extern void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
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extern void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
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unsigned simd;
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simd = x86_simd();
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if (simd & SIMD_SSE4_1)
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ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
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else if (simd & SIMD_SSE2)
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ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
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else abort();
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}
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#endif
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@ -6,12 +6,26 @@
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#ifdef __SSE2__
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#include <emmintrin.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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#endif
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#ifdef KSW_CPU_DISPATCH
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#ifdef __SSE4_1__
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void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez)
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#else
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void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez)
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#endif
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#else
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void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int flag, ksw_extz_t *ez)
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#endif // ~KSW_CPU_DISPATCH
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{
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#define __dp_code_block1 \
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z = _mm_load_si128(&s[t]); \
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|
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@ -6,12 +6,26 @@
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#ifdef __SSE2__
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#include <emmintrin.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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#endif
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#ifdef KSW_CPU_DISPATCH
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#ifdef __SSE4_1__
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void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
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#else
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void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
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#endif
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#else
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void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
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#endif // ~KSW_CPU_DISPATCH
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{
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#define __dp_code_block1 \
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z = _mm_load_si128(&s[t]); \
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|
|
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@ -5,11 +5,23 @@
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#ifdef __SSE2__
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#include <emmintrin.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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#endif
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#ifdef KSW_CPU_DISPATCH
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#ifdef __SSE4_1__
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void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez)
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#else
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void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez)
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#endif
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#else
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void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez)
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#endif // ~KSW_CPU_DISPATCH
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{
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#define __dp_code_block1 \
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z = _mm_add_epi8(_mm_load_si128(&s[t]), qe2_); \
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|
|
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2
main.c
2
main.c
|
|
@ -6,7 +6,7 @@
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|||
#include "mmpriv.h"
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#include "getopt.h"
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||||
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||||
#define MM_VERSION "2.1-r335-dirty"
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#define MM_VERSION "2.1.1-r341"
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||||
|
||||
#ifdef __linux__
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||||
#include <sys/resource.h>
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|
|
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|||
|
|
@ -1,4 +1,4 @@
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|||
.TH minimap2 1 "25 August 2017" "minimap2-2.1-r311" "Bioinformatics tools"
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||||
.TH minimap2 1 "6 September 2017" "minimap2-2.1.1-r341" "Bioinformatics tools"
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||||
.SH NAME
|
||||
.PP
|
||||
minimap2 - mapping and alignment between collections of DNA sequences
|
||||
|
|
|
|||
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