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occ-cutoff
| Author | SHA1 | Date | |
|---|---|---|---|
 Heng Li
|
de6ad4c1d9 | ||
|
Heng Li
|
43b0399991 |
@@ -2,25 +2,13 @@ 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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OBJS_SSE= ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o
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DISPATCH_FLAG=-msse4.1
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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 ($(arm_neon),) # if arm_neon is not defined
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ifeq ($(sse2only),) # if sse2only is not defined
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ifeq ($(avx512),)
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ifeq ($(avx2),)
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OBJS+=$(OBJS_SSE) ksw2_dispatch.o
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else
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OBJS+=ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o
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DISPATCH_FLAG=-mavx2
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endif
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else
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OBJS+=ksw2_extd2_avx512.o ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o
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DISPATCH_FLAG=-mavx512bw
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endif
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
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else # if sse2only is defined
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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@@ -34,16 +22,6 @@ else #if aarch64 is defined
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endif
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endif
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ifneq ($(asan),)
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CFLAGS+=-fsanitize=address
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LIBS+=-fsanitize=address
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endif
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ifneq ($(tsan),)
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CFLAGS+=-fsanitize=thread
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LIBS+=-fsanitize=thread
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endif
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.PHONY:all extra clean depend
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.SUFFIXES:.c .o
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@@ -79,17 +57,11 @@ ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_extd2_avx2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -mavx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extd2_avx512.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -mavx512bw $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 -mno-avx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) -msse4.1 $(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) -msse2 -mno-sse4.1 -mno-avx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(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 $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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@@ -98,7 +70,7 @@ ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(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) $(DISPATCH_FLAG) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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# NEON-specific targets on ARM
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@@ -35,8 +35,6 @@ int main(int argc, char *argv[])
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while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
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mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
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mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
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gzrewind(f);
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kseq_rewind(ks);
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while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
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mm_reg1_t *reg;
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int j, i, n_reg;
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@@ -79,11 +79,11 @@ static char *mm_escape(char *s)
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return s;
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}
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static int sam_write_rg_line(kstring_t *str, const char *s)
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static void sam_write_rg_line(kstring_t *str, const char *s)
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{
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char *p, *q, *r, *rg_line = 0;
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memset(mm_rg_id, 0, 256);
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if (s == 0) return 0;
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if (s == 0) return;
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if (strstr(s, "@RG") != s) {
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if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line is not started with @RG\n");
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goto err_set_rg;
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@@ -108,23 +108,20 @@ static int sam_write_rg_line(kstring_t *str, const char *s)
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for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
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*r++ = *q;
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mm_sprintf_lite(str, "%s\n", rg_line);
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return 0;
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err_set_rg:
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free(rg_line);
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return -1;
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}
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int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
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void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
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{
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kstring_t str = {0,0,0};
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int ret = 0;
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if (idx) {
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uint32_t i;
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for (i = 0; i < idx->n_seq; ++i)
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mm_sprintf_lite(&str, "@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
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}
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if (rg) ret = sam_write_rg_line(&str, rg);
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if (rg) sam_write_rg_line(&str, rg);
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mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
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if (ver) mm_sprintf_lite(&str, "\tVN:%s", ver);
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if (argc > 1) {
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@@ -135,7 +132,6 @@ int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int a
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}
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mm_err_puts(str.s);
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free(str.s);
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return ret;
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}
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static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp, int no_iden, int write_tag)
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@@ -1,4 +1,5 @@
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#include <stdlib.h>
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#include <limits.h>
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#include <assert.h>
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#if defined(WIN32) || defined(_WIN32)
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#include <io.h> // for open(2)
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@@ -117,8 +118,8 @@ void mm_idx_stat(const mm_idx_t *mi)
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if (kh_key(h, k)&1) ++n1;
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}
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}
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fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len);
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fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
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}
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int mm_idx_index_name(mm_idx_t *mi)
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@@ -188,12 +189,18 @@ int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
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* Sort and generate hash tables *
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*********************************/
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typedef struct {
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mm_idx_t *mi;
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int min_occ, max_occ;
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} idx_post_t;
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static void worker_post(void *g, long i, int tid)
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{
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int n, n_keys;
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size_t j, start_a, start_p;
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idxhash_t *h;
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mm_idx_t *mi = (mm_idx_t*)g;
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idx_post_t *o = (idx_post_t*)g;
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mm_idx_t *mi = o->mi;
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mm_idx_bucket_t *b = &mi->B[i];
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if (b->a.n == 0) return;
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@@ -203,8 +210,10 @@ static void worker_post(void *g, long i, int tid)
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// count and preallocate
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for (j = 1, n = 1, n_keys = 0, b->n = 0; j <= b->a.n; ++j) {
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if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
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++n_keys;
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if (n > 1) b->n += n;
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if (n >= o->min_occ && n <= o->max_occ) {
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++n_keys;
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if (n > 1) b->n += n;
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}
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n = 1;
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} else ++n;
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}
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@@ -218,18 +227,20 @@ static void worker_post(void *g, long i, int tid)
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khint_t itr;
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int absent;
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mm128_t *p = &b->a.a[j-1];
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itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
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assert(absent && j == start_a + n);
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if (n == 1) {
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kh_key(h, itr) |= 1;
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kh_val(h, itr) = p->y;
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} else {
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int k;
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for (k = 0; k < n; ++k)
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b->p[start_p + k] = b->a.a[start_a + k].y;
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radix_sort_64(&b->p[start_p], &b->p[start_p + n]); // sort by position; needed as in-place radix_sort_128x() is not stable
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kh_val(h, itr) = (uint64_t)start_p<<32 | n;
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start_p += n;
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if (n >= o->min_occ && n <= o->max_occ) {
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itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
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assert(absent && j == start_a + n);
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if (n == 1) {
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kh_key(h, itr) |= 1;
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kh_val(h, itr) = p->y;
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} else {
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int k;
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for (k = 0; k < n; ++k)
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b->p[start_p + k] = b->a.a[start_a + k].y;
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radix_sort_64(&b->p[start_p], &b->p[start_p + n]); // sort by position; needed as in-place radix_sort_128x() is not stable
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kh_val(h, itr) = (uint64_t)start_p<<32 | n;
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start_p += n;
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}
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}
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start_a = j, n = 1;
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} else ++n;
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@@ -242,9 +253,12 @@ static void worker_post(void *g, long i, int tid)
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b->a.n = b->a.m = 0, b->a.a = 0;
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}
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static void mm_idx_post(mm_idx_t *mi, int n_threads)
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static void mm_idx_post(mm_idx_t *mi, int n_threads, int min_occ, int max_occ)
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{
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kt_for(n_threads, worker_post, mi, 1<<mi->b);
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idx_post_t t;
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if (max_occ <= 0 || max_occ < min_occ) max_occ = INT_MAX;
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t.mi = mi, t.min_occ = min_occ, t.max_occ = max_occ;
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kt_for(n_threads, worker_post, &t, 1<<mi->b);
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}
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/******************
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@@ -350,7 +364,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
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return 0;
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}
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mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size)
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mm_idx_t *mm_idx_gen2(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size, int min_occ, int max_occ)
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{
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pipeline_t pl;
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if (fp == 0 || mm_bseq_eof(fp)) return 0;
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@@ -364,13 +378,18 @@ mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] collected minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
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mm_idx_post(pl.mi, n_threads);
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mm_idx_post(pl.mi, n_threads, min_occ, max_occ);
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] sorted minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
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return pl.mi;
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}
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mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size)
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{
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return mm_idx_gen2(fp, w, k, b, flag, mini_batch_size, n_threads, batch_size, 0, INT_MAX);
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}
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mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads) // a simpler interface; deprecated
|
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{
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mm_bseq_file_t *fp;
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@@ -427,7 +446,7 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
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}
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}
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free(a.a);
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mm_idx_post(mi, 1);
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mm_idx_post(mi, 1, 0, 0);
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return mi;
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}
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@@ -588,7 +607,7 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
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if (mi && mm_verbose >= 2 && (mi->k != r->opt.k || mi->w != r->opt.w || (mi->flag&MM_I_HPC) != (r->opt.flag&MM_I_HPC)))
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fprintf(stderr, "[WARNING]\033[1;31m Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.\033[0m\n");
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} else
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mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
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mi = mm_idx_gen2(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size, r->opt.min_occ, r->opt.max_occ);
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if (mi) {
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if (r->fp_out) mm_idx_dump(r->fp_out, mi);
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mi->index = r->n_parts++;
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+9
-25
@@ -2,16 +2,15 @@
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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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#define SIMD_AVX512BW 0x200
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#define SIMD_SSE 0x1
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#define SIMD_SSE2 0x2
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#define SIMD_SSE3 0x4
|
||||
#define SIMD_SSSE3 0x8
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#define SIMD_SSE4_1 0x10
|
||||
#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
|
||||
|
||||
#ifndef _MSC_VER
|
||||
// adapted from https://github.com/01org/linux-sgx/blob/master/common/inc/internal/linux/cpuid_gnu.h
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@@ -49,7 +48,6 @@ static int x86_simd(void)
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__cpuidex(cpuid, 7, 0);
|
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if (cpuid[1]>>5 &1) flag |= SIMD_AVX2;
|
||||
if (cpuid[1]>>16&1) flag |= SIMD_AVX512F;
|
||||
if (cpuid[1]>>30&1) flag |= SIMD_AVX512BW;
|
||||
}
|
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return flag;
|
||||
}
|
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@@ -73,21 +71,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
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int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
|
||||
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,
|
||||
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
|
||||
extern void ksw_extd2_avx2(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, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
|
||||
extern void ksw_extd2_avx512(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, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
|
||||
if (ksw_simd < 0) ksw_simd = x86_simd();
|
||||
#if defined(__AVX512BW__)
|
||||
if (ksw_simd & SIMD_AVX512BW)
|
||||
ksw_extd2_avx512(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
|
||||
else
|
||||
#endif
|
||||
#if defined(__AVX2__)
|
||||
if (ksw_simd & SIMD_AVX2)
|
||||
ksw_extd2_avx2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
|
||||
else
|
||||
#endif
|
||||
if (ksw_simd & SIMD_SSE4_1)
|
||||
ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
|
||||
else if (ksw_simd & SIMD_SSE2)
|
||||
|
||||
+158
-291
@@ -4,27 +4,7 @@
|
||||
#include "ksw2.h"
|
||||
|
||||
#ifdef __SSE2__
|
||||
|
||||
#if defined(__AVX512BW__)
|
||||
#include <immintrin.h>
|
||||
#define SIMD_INT __m512i
|
||||
#define SIMD_SHIFT 6
|
||||
#define simd_func(func) _mm512_##func
|
||||
#define simd_funcw(func) _mm512_##func##_si512
|
||||
|
||||
#elif defined(__AVX2__)
|
||||
#include <immintrin.h>
|
||||
#define SIMD_INT __m256i
|
||||
#define SIMD_SHIFT 5
|
||||
#define simd_func(func) _mm256_##func
|
||||
#define simd_funcw(func) _mm256_##func##_si256
|
||||
|
||||
#elif defined(__SSE2__)
|
||||
#include <emmintrin.h>
|
||||
#define SIMD_INT __m128i
|
||||
#define SIMD_SHIFT 4
|
||||
#define simd_func(func) _mm_##func
|
||||
#define simd_funcw(func) _mm_##func##_si128
|
||||
|
||||
#ifdef KSW_SSE2_ONLY
|
||||
#undef __SSE4_1__
|
||||
@@ -33,39 +13,12 @@
|
||||
#ifdef __SSE4_1__
|
||||
#include <smmintrin.h>
|
||||
#endif
|
||||
#endif // defined(__SSE2__)
|
||||
|
||||
#define SIMD_WIDTH (1<<SIMD_SHIFT)
|
||||
|
||||
|
||||
#if !defined(__AVX512BW__)
|
||||
#if defined(__AVX2__)
|
||||
static inline __m256i simd_slli_1(__m256i x)
|
||||
{
|
||||
return _mm256_insert_epi8(_mm256_slli_si256(x, 1), _mm256_extract_epi8(x, 15), 16);
|
||||
}
|
||||
static inline __m256i simd_srli_last(__m256i x)
|
||||
{
|
||||
return _mm256_insert_epi8(_mm256_setzero_si256(), _mm256_extract_epi8(x, 31), 0);
|
||||
}
|
||||
#elif defined(__SSE2__)
|
||||
static inline __m128i simd_slli_1(__m128i x) { return _mm_slli_si128(x, 1); }
|
||||
static inline __m128i simd_srli_last(__m128i x) { return _mm_srli_si128(x, 15); }
|
||||
#endif
|
||||
#endif // ~__AVX512BW__
|
||||
|
||||
|
||||
#ifdef KSW_CPU_DISPATCH
|
||||
#if defined(__AVX512BW__)
|
||||
void ksw_extd2_avx512(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, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
|
||||
#elif defined(__AVX2__)
|
||||
void ksw_extd2_avx2(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, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
|
||||
#elif defined(__SSE4_1__)
|
||||
#ifdef __SSE4_1__
|
||||
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,
|
||||
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
|
||||
#elif defined(__SSE2__)
|
||||
#else
|
||||
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,
|
||||
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
|
||||
#endif
|
||||
@@ -74,91 +27,64 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
|
||||
#endif // ~KSW_CPU_DISPATCH
|
||||
{
|
||||
#if defined(__AVX512BW__)
|
||||
#define __dp_code_block1 \
|
||||
z = _mm512_load_si512(&s[t]); \
|
||||
tmp = _mm512_loadu_si512((uint8_t*)&x[t] - 1); \
|
||||
xt1 = _mm512_mask_blend_epi8(1, tmp, x1_); \
|
||||
x1_ = _mm512_maskz_set1_epi8(1, *((uint8_t*)&x[t] + 63)); \
|
||||
tmp = _mm512_loadu_si512((uint8_t*)&v[t] - 1); \
|
||||
vt1 = _mm512_mask_blend_epi8(1, tmp, v1_); \
|
||||
v1_ = _mm512_maskz_set1_epi8(1, *((uint8_t*)&v[t] + 63)); \
|
||||
a = _mm512_add_epi8(xt1, vt1); \
|
||||
ut = _mm512_load_si512(&u[t]); \
|
||||
b = _mm512_add_epi8(_mm512_load_si512(&y[t]), ut); \
|
||||
tmp = _mm512_loadu_si512((uint8_t*)&x2[t] - 1); \
|
||||
x2t1 = _mm512_mask_blend_epi8(1, tmp, x21_); \
|
||||
x21_ = _mm512_maskz_set1_epi8(1, *((uint8_t*)&x2[t] + 63)); \
|
||||
a2= _mm512_add_epi8(x2t1, vt1); \
|
||||
b2= _mm512_add_epi8(_mm512_load_si512(&y2[t]), ut);
|
||||
#else
|
||||
#define __dp_code_block1 \
|
||||
z = simd_funcw(load)(&s[t]); \
|
||||
xt1 = simd_funcw(load)(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
|
||||
tmp = simd_srli_last(xt1); /* tmp <- x[r-1][t+15] */ \
|
||||
xt1 = simd_funcw(or)(simd_slli_1(xt1), x1_); /* xt1 <- x[r-1][t-1..t+14] */ \
|
||||
z = _mm_load_si128(&s[t]); \
|
||||
xt1 = _mm_load_si128(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
|
||||
tmp = _mm_srli_si128(xt1, 15); /* tmp <- x[r-1][t+15] */ \
|
||||
xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_); /* xt1 <- x[r-1][t-1..t+14] */ \
|
||||
x1_ = tmp; \
|
||||
vt1 = simd_funcw(load)(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
|
||||
tmp = simd_srli_last(vt1); /* tmp <- v[r-1][t+15] */ \
|
||||
vt1 = simd_funcw(or)(simd_slli_1(vt1), v1_); /* vt1 <- v[r-1][t-1..t+14] */ \
|
||||
vt1 = _mm_load_si128(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
|
||||
tmp = _mm_srli_si128(vt1, 15); /* tmp <- v[r-1][t+15] */ \
|
||||
vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); /* vt1 <- v[r-1][t-1..t+14] */ \
|
||||
v1_ = tmp; \
|
||||
a = simd_func(add_epi8)(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
|
||||
ut = simd_funcw(load)(&u[t]); /* ut <- u[t..t+15] */ \
|
||||
b = simd_func(add_epi8)(simd_funcw(load)(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */ \
|
||||
x2t1= simd_funcw(load)(&x2[t]); \
|
||||
tmp = simd_srli_last(x2t1); \
|
||||
x2t1= simd_funcw(or)(simd_slli_1(x2t1), x21_); \
|
||||
a = _mm_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
|
||||
ut = _mm_load_si128(&u[t]); /* ut <- u[t..t+15] */ \
|
||||
b = _mm_add_epi8(_mm_load_si128(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */ \
|
||||
x2t1= _mm_load_si128(&x2[t]); \
|
||||
tmp = _mm_srli_si128(x2t1, 15); \
|
||||
x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); \
|
||||
x21_= tmp; \
|
||||
a2= simd_func(add_epi8)(x2t1, vt1); \
|
||||
b2= simd_func(add_epi8)(simd_funcw(load)(&y2[t]), ut);
|
||||
#endif // ~__AVX512BW__
|
||||
a2= _mm_add_epi8(x2t1, vt1); \
|
||||
b2= _mm_add_epi8(_mm_load_si128(&y2[t]), ut);
|
||||
|
||||
#define __dp_code_block2 \
|
||||
simd_funcw(store)(&u[t], simd_func(sub_epi8)(z, vt1));/* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
|
||||
simd_funcw(store)(&v[t], simd_func(sub_epi8)(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
|
||||
tmp = simd_func(sub_epi8)(z, q_); \
|
||||
a = simd_func(sub_epi8)(a, tmp); \
|
||||
b = simd_func(sub_epi8)(b, tmp); \
|
||||
tmp = simd_func(sub_epi8)(z, q2_); \
|
||||
a2= simd_func(sub_epi8)(a2, tmp); \
|
||||
b2= simd_func(sub_epi8)(b2, tmp);
|
||||
_mm_store_si128(&u[t], _mm_sub_epi8(z, vt1)); /* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
|
||||
_mm_store_si128(&v[t], _mm_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
|
||||
tmp = _mm_sub_epi8(z, q_); \
|
||||
a = _mm_sub_epi8(a, tmp); \
|
||||
b = _mm_sub_epi8(b, tmp); \
|
||||
tmp = _mm_sub_epi8(z, q2_); \
|
||||
a2= _mm_sub_epi8(a2, tmp); \
|
||||
b2= _mm_sub_epi8(b2, tmp);
|
||||
|
||||
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc, min_sc, long_thres, long_diff;
|
||||
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
|
||||
int32_t *H = 0, H0 = 0, last_H0_t = 0;
|
||||
uint8_t *qr, *sf, *mem, *mem2 = 0;
|
||||
SIMD_INT q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_, mask1_;
|
||||
SIMD_INT *u, *v, *x, *y, *x2, *y2, *s, *p = 0;
|
||||
__m128i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_;
|
||||
__m128i *u, *v, *x, *y, *x2, *y2, *s, *p = 0;
|
||||
|
||||
ksw_reset_extz(ez);
|
||||
if (m <= 1 || qlen <= 0 || tlen <= 0) return;
|
||||
|
||||
if (q2 + e2 < q + e) t = q, q = q2, q2 = t, t = e, e = e2, e2 = t; // make sure q+e no larger than q2+e2
|
||||
|
||||
zero_ = simd_func(set1_epi8)(0);
|
||||
q_ = simd_func(set1_epi8)(q);
|
||||
q2_ = simd_func(set1_epi8)(q2);
|
||||
qe_ = simd_func(set1_epi8)(q + e);
|
||||
qe2_ = simd_func(set1_epi8)(q2 + e2);
|
||||
sc_mch_ = simd_func(set1_epi8)(mat[0]);
|
||||
sc_mis_ = simd_func(set1_epi8)(mat[1]);
|
||||
sc_N_ = mat[m*m-1] == 0? simd_func(set1_epi8)(-e2) : simd_func(set1_epi8)(mat[m*m-1]);
|
||||
m1_ = simd_func(set1_epi8)(m - 1); // wildcard
|
||||
|
||||
#if defined(__AVX512BW__)
|
||||
mask1_ = _mm512_maskz_set1_epi8(1, 0xff);
|
||||
#elif defined(__AVX2__)
|
||||
mask1_ = _mm256_setr_epi32(0xff, 0, 0, 0, 0, 0, 0, 0);
|
||||
#elif defined(__SSE2__)
|
||||
mask1_ = _mm_setr_epi32(0xff, 0, 0, 0);
|
||||
#endif
|
||||
zero_ = _mm_set1_epi8(0);
|
||||
q_ = _mm_set1_epi8(q);
|
||||
q2_ = _mm_set1_epi8(q2);
|
||||
qe_ = _mm_set1_epi8(q + e);
|
||||
qe2_ = _mm_set1_epi8(q2 + e2);
|
||||
sc_mch_ = _mm_set1_epi8(mat[0]);
|
||||
sc_mis_ = _mm_set1_epi8(mat[1]);
|
||||
sc_N_ = mat[m*m-1] == 0? _mm_set1_epi8(-e2) : _mm_set1_epi8(mat[m*m-1]);
|
||||
m1_ = _mm_set1_epi8(m - 1); // wildcard
|
||||
|
||||
if (w < 0) w = tlen > qlen? tlen : qlen;
|
||||
wl = wr = w;
|
||||
tlen_ = (tlen + SIMD_WIDTH - 1) / SIMD_WIDTH;
|
||||
tlen_ = (tlen + 15) / 16;
|
||||
n_col_ = qlen < tlen? qlen : tlen;
|
||||
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + SIMD_WIDTH - 1) / SIMD_WIDTH + 1;
|
||||
qlen_ = (qlen + SIMD_WIDTH - 1) / SIMD_WIDTH;
|
||||
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 15) / 16 + 1;
|
||||
qlen_ = (qlen + 15) / 16;
|
||||
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
|
||||
max_sc = max_sc > mat[t]? max_sc : mat[t];
|
||||
min_sc = min_sc < mat[t]? min_sc : mat[t];
|
||||
@@ -170,23 +96,23 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
++long_thres;
|
||||
long_diff = long_thres * (e - e2) - (q2 - q) - e2;
|
||||
|
||||
mem = (uint8_t*)kcalloc(km, tlen_ * 8 + qlen_ + 1, SIMD_WIDTH);
|
||||
u = (SIMD_INT*)(((size_t)mem + SIMD_WIDTH - 1) >> SIMD_SHIFT << SIMD_SHIFT); // 16-byte aligned
|
||||
mem = (uint8_t*)kcalloc(km, tlen_ * 8 + qlen_ + 1, 16);
|
||||
u = (__m128i*)(((size_t)mem + 15) >> 4 << 4); // 16-byte aligned
|
||||
v = u + tlen_, x = v + tlen_, y = x + tlen_, x2 = y + tlen_, y2 = x2 + tlen_;
|
||||
s = y2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * SIMD_WIDTH;
|
||||
memset(u, -q - e, tlen_ * SIMD_WIDTH);
|
||||
memset(v, -q - e, tlen_ * SIMD_WIDTH);
|
||||
memset(x, -q - e, tlen_ * SIMD_WIDTH);
|
||||
memset(y, -q - e, tlen_ * SIMD_WIDTH);
|
||||
memset(x2, -q2 - e2, tlen_ * SIMD_WIDTH);
|
||||
memset(y2, -q2 - e2, tlen_ * SIMD_WIDTH);
|
||||
s = y2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 16;
|
||||
memset(u, -q - e, tlen_ * 16);
|
||||
memset(v, -q - e, tlen_ * 16);
|
||||
memset(x, -q - e, tlen_ * 16);
|
||||
memset(y, -q - e, tlen_ * 16);
|
||||
memset(x2, -q2 - e2, tlen_ * 16);
|
||||
memset(y2, -q2 - e2, tlen_ * 16);
|
||||
if (!approx_max) {
|
||||
H = (int32_t*)kmalloc(km, tlen_ * SIMD_WIDTH * 4);
|
||||
for (t = 0; t < tlen_ * SIMD_WIDTH; ++t) H[t] = KSW_NEG_INF;
|
||||
H = (int32_t*)kmalloc(km, tlen_ * 16 * 4);
|
||||
for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
|
||||
}
|
||||
if (with_cigar) {
|
||||
mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * SIMD_WIDTH);
|
||||
p = (SIMD_INT*)(((size_t)mem2 + SIMD_WIDTH - 1) >> SIMD_SHIFT << SIMD_SHIFT);
|
||||
mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 16);
|
||||
p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
|
||||
off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
|
||||
off_end = off + qlen + tlen - 1;
|
||||
}
|
||||
@@ -199,7 +125,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
int8_t x1, x21, v1;
|
||||
uint8_t *qrr = qr + (qlen - 1 - r);
|
||||
int8_t *u8 = (int8_t*)u, *v8 = (int8_t*)v, *x8 = (int8_t*)x, *x28 = (int8_t*)x2;
|
||||
SIMD_INT x1_, x21_, v1_;
|
||||
__m128i x1_, x21_, v1_;
|
||||
// find the boundaries
|
||||
if (st < r - qlen + 1) st = r - qlen + 1;
|
||||
if (en > r) en = r;
|
||||
@@ -210,7 +136,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
break;
|
||||
}
|
||||
st0 = st, en0 = en;
|
||||
st = st / SIMD_WIDTH * SIMD_WIDTH, en = (en + SIMD_WIDTH) / SIMD_WIDTH * SIMD_WIDTH - 1;
|
||||
st = st / 16 * 16, en = (en + 16) / 16 * 16 - 1;
|
||||
// set boundary conditions
|
||||
if (st > 0) {
|
||||
if (st - 1 >= last_st && st - 1 <= last_en) {
|
||||
@@ -229,53 +155,47 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
}
|
||||
// loop fission: set scores first
|
||||
if (!(flag & KSW_EZ_GENERIC_SC)) {
|
||||
for (t = st0; t <= en0; t += SIMD_WIDTH) {
|
||||
SIMD_INT sq, st, tmp;
|
||||
sq = simd_funcw(loadu)((SIMD_INT*)&sf[t]);
|
||||
st = simd_funcw(loadu)((SIMD_INT*)&qrr[t]);
|
||||
#if defined(__AVX512BW__)
|
||||
__mmask64 mask = _mm512_cmpeq_epi8_mask(sq, m1_) | _mm512_cmpeq_epi8_mask(st, m1_);
|
||||
tmp = _mm512_mask_blend_epi8(_mm512_cmpeq_epi8_mask(sq, st), sc_mis_, sc_mch_);
|
||||
tmp = _mm512_mask_blend_epi8(mask, tmp, sc_N_);
|
||||
#elif defined(__SSE4_1__) || defined(__AVX2__)
|
||||
SIMD_INT mask = simd_funcw(or)(simd_func(cmpeq_epi8)(sq, m1_), simd_func(cmpeq_epi8)(st, m1_));
|
||||
tmp = simd_func(cmpeq_epi8)(sq, st);
|
||||
tmp = simd_func(blendv_epi8)(sc_mis_, sc_mch_, tmp);
|
||||
tmp = simd_func(blendv_epi8)(tmp, sc_N_, mask);
|
||||
#elif defined(__SSE2__) // emulate blendv
|
||||
SIMD_INT mask = simd_funcw(or)(simd_func(cmpeq_epi8)(sq, m1_), simd_func(cmpeq_epi8)(st, m1_));
|
||||
tmp = simd_func(cmpeq_epi8)(sq, st);
|
||||
for (t = st0; t <= en0; t += 16) {
|
||||
__m128i sq, st, tmp, mask;
|
||||
sq = _mm_loadu_si128((__m128i*)&sf[t]);
|
||||
st = _mm_loadu_si128((__m128i*)&qrr[t]);
|
||||
mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
|
||||
tmp = _mm_cmpeq_epi8(sq, st);
|
||||
#ifdef __SSE4_1__
|
||||
tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);
|
||||
tmp = _mm_blendv_epi8(tmp, sc_N_, mask);
|
||||
#else
|
||||
tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));
|
||||
tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp), _mm_and_si128(mask, sc_N_));
|
||||
#endif
|
||||
simd_funcw(storeu)((SIMD_INT*)((int8_t*)s + t), tmp);
|
||||
_mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);
|
||||
}
|
||||
} else {
|
||||
for (t = st0; t <= en0; ++t)
|
||||
((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
|
||||
}
|
||||
// core loop
|
||||
x1_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)x1), mask1_);
|
||||
x21_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)x21), mask1_);
|
||||
v1_ = simd_funcw(and)(simd_func(set1_epi8)((uint8_t)v1), mask1_);
|
||||
st_ = st / SIMD_WIDTH, en_ = en / SIMD_WIDTH;
|
||||
x1_ = _mm_cvtsi32_si128((uint8_t)x1);
|
||||
x21_ = _mm_cvtsi32_si128((uint8_t)x21);
|
||||
v1_ = _mm_cvtsi32_si128((uint8_t)v1);
|
||||
st_ = st / 16, en_ = en / 16;
|
||||
assert(en_ - st_ + 1 <= n_col_);
|
||||
if (!with_cigar) { // score only
|
||||
for (t = st_; t <= en_; ++t) {
|
||||
SIMD_INT z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__dp_code_block1;
|
||||
#if defined(__SSE4_1__) || defined(__AVX2__) || defined(__AVX512BW__)
|
||||
z = simd_func(max_epi8)(z, a);
|
||||
z = simd_func(max_epi8)(z, b);
|
||||
z = simd_func(max_epi8)(z, a2);
|
||||
z = simd_func(max_epi8)(z, b2);
|
||||
z = simd_func(min_epi8)(z, sc_mch_);
|
||||
#ifdef __SSE4_1__
|
||||
z = _mm_max_epi8(z, a);
|
||||
z = _mm_max_epi8(z, b);
|
||||
z = _mm_max_epi8(z, a2);
|
||||
z = _mm_max_epi8(z, b2);
|
||||
z = _mm_min_epi8(z, sc_mch_);
|
||||
__dp_code_block2; // save u[] and v[]; update a, b, a2 and b2
|
||||
simd_funcw(store)(&x[t], simd_func(sub_epi8)(simd_func(max_epi8)(a, zero_), qe_));
|
||||
simd_funcw(store)(&y[t], simd_func(sub_epi8)(simd_func(max_epi8)(b, zero_), qe_));
|
||||
simd_funcw(store)(&x2[t], simd_func(sub_epi8)(simd_func(max_epi8)(a2, zero_), qe2_));
|
||||
simd_funcw(store)(&y2[t], simd_func(sub_epi8)(simd_func(max_epi8)(b2, zero_), qe2_));
|
||||
#elif defined(__SSE2__)
|
||||
_mm_store_si128(&x[t], _mm_sub_epi8(_mm_max_epi8(a, zero_), qe_));
|
||||
_mm_store_si128(&y[t], _mm_sub_epi8(_mm_max_epi8(b, zero_), qe_));
|
||||
_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, zero_), qe2_));
|
||||
_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_max_epi8(b2, zero_), qe2_));
|
||||
#else
|
||||
tmp = _mm_cmpgt_epi8(a, z);
|
||||
z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));
|
||||
tmp = _mm_cmpgt_epi8(b, z);
|
||||
@@ -298,42 +218,22 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
#endif
|
||||
}
|
||||
} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
|
||||
SIMD_INT *pr = p + (size_t)r * n_col_ - st_;
|
||||
__m128i *pr = p + (size_t)r * n_col_ - st_;
|
||||
off[r] = st, off_end[r] = en;
|
||||
for (t = st_; t <= en_; ++t) {
|
||||
SIMD_INT d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__dp_code_block1;
|
||||
#if defined(__AVX512BW__)
|
||||
d = _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a, z), 1);
|
||||
z = _mm512_max_epi8(z, a);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, _mm512_set1_epi8(2));
|
||||
z = _mm512_max_epi8(z, b);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, _mm512_set1_epi8(3));
|
||||
z = _mm512_max_epi8(z, a2);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, _mm512_set1_epi8(4));
|
||||
z = _mm512_max_epi8(z, b2);
|
||||
z = _mm512_min_epi8(z, sc_mch_);
|
||||
__dp_code_block2;
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a, zero_), 0x08)); // d = a > 0? 1<<3 : 0
|
||||
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b, zero_), 0x10)); // d = b > 0? 1<<4 : 0
|
||||
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a2, zero_), 0x20)); // d = a2 > 0? 1<<5 : 0
|
||||
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b2, zero_), 0x40)); // d = b2 > 0? 1<<6 : 0
|
||||
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
|
||||
#else
|
||||
#if defined(__SSE4_1__) || defined(__AVX2__)
|
||||
d = simd_funcw(and)(simd_func(cmpgt_epi8)(a, z), simd_func(set1_epi8)(1)); // d = a > z? 1 : 0
|
||||
z = simd_func(max_epi8)(z, a);
|
||||
d = simd_func(blendv_epi8)(d, simd_func(set1_epi8)(2), simd_func(cmpgt_epi8)(b, z)); // d = b > z? 2 : d
|
||||
z = simd_func(max_epi8)(z, b);
|
||||
d = simd_func(blendv_epi8)(d, simd_func(set1_epi8)(3), simd_func(cmpgt_epi8)(a2, z)); // d = a2 > z? 3 : d
|
||||
z = simd_func(max_epi8)(z, a2);
|
||||
d = simd_func(blendv_epi8)(d, simd_func(set1_epi8)(4), simd_func(cmpgt_epi8)(b2, z)); // d = a2 > z? 3 : d
|
||||
z = simd_func(max_epi8)(z, b2);
|
||||
z = simd_func(min_epi8)(z, sc_mch_);
|
||||
#elif defined(__SSE2__) // emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
|
||||
#ifdef __SSE4_1__
|
||||
d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1)); // d = a > z? 1 : 0
|
||||
z = _mm_max_epi8(z, a);
|
||||
d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b, z)); // d = b > z? 2 : d
|
||||
z = _mm_max_epi8(z, b);
|
||||
d = _mm_blendv_epi8(d, _mm_set1_epi8(3), _mm_cmpgt_epi8(a2, z)); // d = a2 > z? 3 : d
|
||||
z = _mm_max_epi8(z, a2);
|
||||
d = _mm_blendv_epi8(d, _mm_set1_epi8(4), _mm_cmpgt_epi8(b2, z)); // d = a2 > z? 3 : d
|
||||
z = _mm_max_epi8(z, b2);
|
||||
z = _mm_min_epi8(z, sc_mch_);
|
||||
#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
|
||||
tmp = _mm_cmpgt_epi8(a, z);
|
||||
d = _mm_and_si128(tmp, _mm_set1_epi8(1));
|
||||
z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));
|
||||
@@ -348,60 +248,39 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));
|
||||
tmp = _mm_cmplt_epi8(sc_mch_, z);
|
||||
z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
|
||||
#endif // ~__SSE2__
|
||||
#endif
|
||||
__dp_code_block2;
|
||||
tmp = simd_func(cmpgt_epi8)(a, zero_);
|
||||
simd_funcw(store)(&x[t], simd_func(sub_epi8)(simd_funcw(and)(tmp, a), qe_));
|
||||
d = simd_funcw(or)(d, simd_funcw(and)(tmp, simd_func(set1_epi8)(0x08))); // d = a > 0? 1<<3 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(b, zero_);
|
||||
simd_funcw(store)(&y[t], simd_func(sub_epi8)(simd_funcw(and)(tmp, b), qe_));
|
||||
d = simd_funcw(or)(d, simd_funcw(and)(tmp, simd_func(set1_epi8)(0x10))); // d = b > 0? 1<<4 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(a2, zero_);
|
||||
simd_funcw(store)(&x2[t], simd_func(sub_epi8)(simd_funcw(and)(tmp, a2), qe2_));
|
||||
d = simd_funcw(or)(d, simd_funcw(and)(tmp, simd_func(set1_epi8)(0x20))); // d = a > 0? 1<<5 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(b2, zero_);
|
||||
simd_funcw(store)(&y2[t], simd_func(sub_epi8)(simd_funcw(and)(tmp, b2), qe2_));
|
||||
d = simd_funcw(or)(d, simd_funcw(and)(tmp, simd_func(set1_epi8)(0x40))); // d = b > 0? 1<<6 : 0
|
||||
#endif // ~__AVX512BW__
|
||||
simd_funcw(store)(&pr[t], d);
|
||||
tmp = _mm_cmpgt_epi8(a, zero_);
|
||||
_mm_store_si128(&x[t], _mm_sub_epi8(_mm_and_si128(tmp, a), qe_));
|
||||
d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0
|
||||
tmp = _mm_cmpgt_epi8(b, zero_);
|
||||
_mm_store_si128(&y[t], _mm_sub_epi8(_mm_and_si128(tmp, b), qe_));
|
||||
d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0
|
||||
tmp = _mm_cmpgt_epi8(a2, zero_);
|
||||
_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), qe2_));
|
||||
d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
|
||||
tmp = _mm_cmpgt_epi8(b2, zero_);
|
||||
_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_and_si128(tmp, b2), qe2_));
|
||||
d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x40))); // d = b > 0? 1<<6 : 0
|
||||
_mm_store_si128(&pr[t], d);
|
||||
}
|
||||
} else { // gap right-alignment
|
||||
SIMD_INT *pr = p + (size_t)r * n_col_ - st_;
|
||||
__m128i *pr = p + (size_t)r * n_col_ - st_;
|
||||
off[r] = st, off_end[r] = en;
|
||||
for (t = st_; t <= en_; ++t) {
|
||||
SIMD_INT d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
|
||||
__dp_code_block1;
|
||||
#if defined(__AVX512BW__)
|
||||
d = _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a, z), 1);
|
||||
z = _mm512_max_epi8(z, a);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpge_epi8_mask(b, z), d, _mm512_set1_epi8(2));
|
||||
z = _mm512_max_epi8(z, b);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpge_epi8_mask(a2, z), d, _mm512_set1_epi8(3));
|
||||
z = _mm512_max_epi8(z, a2);
|
||||
d = _mm512_mask_blend_epi8(_mm512_cmpge_epi8_mask(b2, z), d, _mm512_set1_epi8(4));
|
||||
z = _mm512_max_epi8(z, b2);
|
||||
z = _mm512_min_epi8(z, sc_mch_);
|
||||
__dp_code_block2;
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a, zero_), 0x08)); // d = a >= 0? 1<<3 : 0
|
||||
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b, zero_), 0x10)); // d = b >= 0? 1<<4 : 0
|
||||
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a2, zero_), 0x20)); // d = a2 >= 0? 1<<5 : 0
|
||||
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_));
|
||||
d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b2, zero_), 0x40)); // d = b2 >= 0? 1<<6 : 0
|
||||
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
|
||||
#else
|
||||
#if defined(__SSE4_1__) || defined(__AVX2__)
|
||||
d = simd_funcw(andnot)(simd_func(cmpgt_epi8)(z, a), simd_func(set1_epi8)(1)); // d = z > a? 0 : 1
|
||||
z = simd_func(max_epi8)(z, a);
|
||||
d = simd_func(blendv_epi8)(simd_func(set1_epi8)(2), d, simd_func(cmpgt_epi8)(z, b)); // d = z > b? d : 2
|
||||
z = simd_func(max_epi8)(z, b);
|
||||
d = simd_func(blendv_epi8)(simd_func(set1_epi8)(3), d, simd_func(cmpgt_epi8)(z, a2)); // d = z > a2? d : 3
|
||||
z = simd_func(max_epi8)(z, a2);
|
||||
d = simd_func(blendv_epi8)(simd_func(set1_epi8)(4), d, simd_func(cmpgt_epi8)(z, b2)); // d = z > b2? d : 4
|
||||
z = simd_func(max_epi8)(z, b2);
|
||||
z = simd_func(min_epi8)(z, sc_mch_);
|
||||
#elif defined(__SSE2__)
|
||||
#ifdef __SSE4_1__
|
||||
d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1)); // d = z > a? 0 : 1
|
||||
z = _mm_max_epi8(z, a);
|
||||
d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b)); // d = z > b? d : 2
|
||||
z = _mm_max_epi8(z, b);
|
||||
d = _mm_blendv_epi8(_mm_set1_epi8(3), d, _mm_cmpgt_epi8(z, a2)); // d = z > a2? d : 3
|
||||
z = _mm_max_epi8(z, a2);
|
||||
d = _mm_blendv_epi8(_mm_set1_epi8(4), d, _mm_cmpgt_epi8(z, b2)); // d = z > b2? d : 4
|
||||
z = _mm_max_epi8(z, b2);
|
||||
z = _mm_min_epi8(z, sc_mch_);
|
||||
#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()
|
||||
tmp = _mm_cmpgt_epi8(z, a);
|
||||
d = _mm_andnot_si128(tmp, _mm_set1_epi8(1));
|
||||
z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a));
|
||||
@@ -416,64 +295,52 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b2));
|
||||
tmp = _mm_cmplt_epi8(sc_mch_, z);
|
||||
z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));
|
||||
#endif // ~__SSE2__
|
||||
#endif
|
||||
__dp_code_block2;
|
||||
tmp = simd_func(cmpgt_epi8)(zero_, a);
|
||||
simd_funcw(store)(&x[t], simd_func(sub_epi8)(simd_funcw(andnot)(tmp, a), qe_));
|
||||
d = simd_funcw(or)(d, simd_funcw(andnot)(tmp, simd_func(set1_epi8)(0x08))); // d = a > 0? 1<<3 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(zero_, b);
|
||||
simd_funcw(store)(&y[t], simd_func(sub_epi8)(simd_funcw(andnot)(tmp, b), qe_));
|
||||
d = simd_funcw(or)(d, simd_funcw(andnot)(tmp, simd_func(set1_epi8)(0x10))); // d = b > 0? 1<<4 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(zero_, a2);
|
||||
simd_funcw(store)(&x2[t], simd_func(sub_epi8)(simd_funcw(andnot)(tmp, a2), qe2_));
|
||||
d = simd_funcw(or)(d, simd_funcw(andnot)(tmp, simd_func(set1_epi8)(0x20))); // d = a > 0? 1<<5 : 0
|
||||
tmp = simd_func(cmpgt_epi8)(zero_, b2);
|
||||
simd_funcw(store)(&y2[t], simd_func(sub_epi8)(simd_funcw(andnot)(tmp, b2), qe2_));
|
||||
d = simd_funcw(or)(d, simd_funcw(andnot)(tmp, simd_func(set1_epi8)(0x40))); // d = b > 0? 1<<6 : 0
|
||||
#endif // ~__AVX512BW__
|
||||
simd_funcw(store)(&pr[t], d);
|
||||
tmp = _mm_cmpgt_epi8(zero_, a);
|
||||
_mm_store_si128(&x[t], _mm_sub_epi8(_mm_andnot_si128(tmp, a), qe_));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0
|
||||
tmp = _mm_cmpgt_epi8(zero_, b);
|
||||
_mm_store_si128(&y[t], _mm_sub_epi8(_mm_andnot_si128(tmp, b), qe_));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0
|
||||
tmp = _mm_cmpgt_epi8(zero_, a2);
|
||||
_mm_store_si128(&x2[t], _mm_sub_epi8(_mm_andnot_si128(tmp, a2), qe2_));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
|
||||
tmp = _mm_cmpgt_epi8(zero_, b2);
|
||||
_mm_store_si128(&y2[t], _mm_sub_epi8(_mm_andnot_si128(tmp, b2), qe2_));
|
||||
d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x40))); // d = b > 0? 1<<6 : 0
|
||||
_mm_store_si128(&pr[t], d);
|
||||
}
|
||||
}
|
||||
if (!approx_max) { // find the exact max with a 32-bit score array
|
||||
int32_t max_H, max_t;
|
||||
// compute H[], max_H and max_t
|
||||
if (r > 0) {
|
||||
int32_t HH[SIMD_WIDTH/4], tt[SIMD_WIDTH/4], en1 = st0 + (en0 - st0) / (SIMD_WIDTH/4) * (SIMD_WIDTH/4), i;
|
||||
SIMD_INT max_H_, max_t_;
|
||||
int32_t HH[4], tt[4], en1 = st0 + (en0 - st0) / 4 * 4, i;
|
||||
__m128i max_H_, max_t_;
|
||||
max_H = H[en0] = en0 > 0? H[en0-1] + u8[en0] : H[en0] + v8[en0]; // special casing the last element
|
||||
max_t = en0;
|
||||
max_H_ = simd_func(set1_epi32)(max_H);
|
||||
max_t_ = simd_func(set1_epi32)(max_t);
|
||||
for (t = st0; t < en1; t += SIMD_WIDTH/4) { // this implements: H[t]+=v8[t]; if(H[t]>max_H) max_H=H[t],max_t=t;
|
||||
SIMD_INT H1, t_;
|
||||
H1 = simd_funcw(loadu)((SIMD_INT*)&H[t]);
|
||||
#if defined(__AVX512BW__)
|
||||
t_ = _mm512_cvtepi8_epi32(_mm_loadu_si128((__m128i*)&v8[t]));
|
||||
#elif defined(__AVX2__)
|
||||
t_ = _mm256_setr_epi32(v8[t], v8[t+1], v8[t+2], v8[t+3], v8[t+4], v8[t+5], v8[t+6], v8[t+7]);
|
||||
#elif defined(__SSE2__)
|
||||
max_H_ = _mm_set1_epi32(max_H);
|
||||
max_t_ = _mm_set1_epi32(max_t);
|
||||
for (t = st0; t < en1; t += 4) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
|
||||
__m128i H1, tmp, t_;
|
||||
H1 = _mm_loadu_si128((__m128i*)&H[t]);
|
||||
t_ = _mm_setr_epi32(v8[t], v8[t+1], v8[t+2], v8[t+3]);
|
||||
#endif
|
||||
H1 = simd_func(add_epi32)(H1, t_);
|
||||
simd_funcw(storeu)((SIMD_INT*)&H[t], H1);
|
||||
t_ = simd_func(set1_epi32)(t);
|
||||
#if defined(__AVX512BW__)
|
||||
__mmask64 tmp = _mm512_cmpgt_epi32_mask(H1, max_H_);
|
||||
max_H_ = _mm512_mask_blend_epi32(tmp, max_H_, H1);
|
||||
max_t_ = _mm512_mask_blend_epi32(tmp, max_t_, t_);
|
||||
#elif defined(__SSE4_1__) || defined(__AVX2__)
|
||||
SIMD_INT tmp = simd_func(cmpgt_epi32)(H1, max_H_);
|
||||
max_H_ = simd_func(blendv_epi8)(max_H_, H1, tmp);
|
||||
max_t_ = simd_func(blendv_epi8)(max_t_, t_, tmp);
|
||||
#elif defined(__SSE2__)
|
||||
SIMD_INT tmp = simd_func(cmpgt_epi32)(H1, max_H_);
|
||||
max_H_ = simd_funcw(or)(simd_funcw(and)(tmp, H1), simd_funcw(andnot)(tmp, max_H_));
|
||||
max_t_ = simd_funcw(or)(simd_funcw(and)(tmp, t_), simd_funcw(andnot)(tmp, max_t_));
|
||||
H1 = _mm_add_epi32(H1, t_);
|
||||
_mm_storeu_si128((__m128i*)&H[t], H1);
|
||||
t_ = _mm_set1_epi32(t);
|
||||
tmp = _mm_cmpgt_epi32(H1, max_H_);
|
||||
#ifdef __SSE4_1__
|
||||
max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);
|
||||
max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);
|
||||
#else
|
||||
max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));
|
||||
max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));
|
||||
#endif
|
||||
}
|
||||
simd_funcw(storeu)((SIMD_INT*)HH, max_H_);
|
||||
simd_funcw(storeu)((SIMD_INT*)tt, max_t_);
|
||||
for (i = 0; i < SIMD_WIDTH/4; ++i)
|
||||
_mm_storeu_si128((__m128i*)HH, max_H_);
|
||||
_mm_storeu_si128((__m128i*)tt, max_t_);
|
||||
for (i = 0; i < 4; ++i)
|
||||
if (max_H < HH[i]) max_H = HH[i], max_t = tt[i] + i;
|
||||
for (; t < en0; ++t) { // for the rest of values that haven't been computed with SSE
|
||||
H[t] += (int32_t)v8[t];
|
||||
@@ -514,12 +381,12 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
|
||||
if (with_cigar) { // backtrack
|
||||
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
|
||||
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*SIMD_WIDTH, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
|
||||
ez->reach_end = 1;
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*SIMD_WIDTH, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
} else if (ez->max_t >= 0 && ez->max_q >= 0) {
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*SIMD_WIDTH, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
|
||||
}
|
||||
kfree(km, mem2); kfree(km, off);
|
||||
}
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
#include "mmpriv.h"
|
||||
#include "ketopt.h"
|
||||
|
||||
#define MM_VERSION "2.17-r963-dirty"
|
||||
#define MM_VERSION "2.17-r954-dirty"
|
||||
|
||||
#ifdef __linux__
|
||||
#include <sys/resource.h>
|
||||
@@ -67,6 +67,10 @@ static ko_longopt_t long_options[] = {
|
||||
{ "junc-bed", ko_required_argument, 340 },
|
||||
{ "junc-bonus", ko_required_argument, 341 },
|
||||
{ "sam-hit-only", ko_no_argument, 342 },
|
||||
{ "idx-min-occ", ko_required_argument, 343 },
|
||||
{ "idx-max-occ", ko_required_argument, 344 },
|
||||
{ "flt-max-dv", ko_required_argument, 345 },
|
||||
{ "flt-min-blen", ko_required_argument, 346 },
|
||||
{ "help", ko_no_argument, 'h' },
|
||||
{ "max-intron-len", ko_required_argument, 'G' },
|
||||
{ "version", ko_no_argument, 'V' },
|
||||
@@ -209,8 +213,11 @@ int main(int argc, char *argv[])
|
||||
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
|
||||
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
|
||||
else if (c == 340) junc_bed = o.arg; // --junc-bed
|
||||
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
|
||||
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
|
||||
else if (c == 343) ipt.min_occ = mm_parse_num(o.arg); // --idx-min-occ
|
||||
else if (c == 344) ipt.max_occ = mm_parse_num(o.arg); // --idx-max-occ
|
||||
else if (c == 345) opt.flt_max_dv = atof(o.arg); // --flt-max-dv
|
||||
else if (c == 346) opt.flt_min_blen = mm_parse_num(o.arg); // --flt-min-blen
|
||||
else if (c == 314) { // --frag
|
||||
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
|
||||
} else if (c == 315) { // --secondary
|
||||
@@ -324,11 +331,11 @@ int main(int argc, char *argv[])
|
||||
fprintf(fp_help, " --version show version number\n");
|
||||
fprintf(fp_help, " Preset:\n");
|
||||
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
|
||||
fprintf(fp_help, " - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
|
||||
fprintf(fp_help, " - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
|
||||
fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
|
||||
fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
|
||||
fprintf(fp_help, " - sr - genomic short-read mapping\n");
|
||||
fprintf(fp_help, " - map-pb/map-ont: PacBio/Nanopore vs reference mapping\n");
|
||||
fprintf(fp_help, " - ava-pb/ava-ont: PacBio/Nanopore read overlap\n");
|
||||
fprintf(fp_help, " - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
|
||||
fprintf(fp_help, " - splice: long-read spliced alignment\n");
|
||||
fprintf(fp_help, " - sr: genomic short-read mapping\n");
|
||||
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of these and other advanced command-line options.\n");
|
||||
return fp_help == stdout? 0 : 1;
|
||||
}
|
||||
@@ -357,19 +364,13 @@ int main(int argc, char *argv[])
|
||||
return 1;
|
||||
}
|
||||
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
|
||||
int ret;
|
||||
if (mm_idx_reader_eof(idx_rdr)) {
|
||||
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
|
||||
mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
|
||||
} else {
|
||||
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
|
||||
mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
|
||||
if (opt.split_prefix == 0 && mm_verbose >= 2)
|
||||
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
|
||||
}
|
||||
if (ret != 0) {
|
||||
mm_idx_destroy(mi);
|
||||
mm_idx_reader_close(idx_rdr);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
if (mm_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
|
||||
|
||||
@@ -351,6 +351,15 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
|
||||
|
||||
chain_post(opt, max_chain_gap_ref, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
|
||||
if (!is_sr) mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
|
||||
if (!is_sr && n_segs == 1) {
|
||||
for (i = j = 0; i < n_regs0; ++i) {
|
||||
mm_reg1_t *r = ®s0[i];
|
||||
if (r->div > opt->flt_max_dv) continue;
|
||||
if (r->blen < opt->flt_min_blen) continue;
|
||||
regs0[j++] = regs0[i];
|
||||
}
|
||||
n_regs0 = j;
|
||||
}
|
||||
|
||||
if (n_segs == 1) { // uni-segment
|
||||
regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);
|
||||
|
||||
@@ -101,6 +101,7 @@ typedef struct {
|
||||
typedef struct {
|
||||
short k, w, flag, bucket_bits;
|
||||
int mini_batch_size;
|
||||
int min_occ, max_occ;
|
||||
uint64_t batch_size;
|
||||
} mm_idxopt_t;
|
||||
|
||||
@@ -118,6 +119,9 @@ typedef struct {
|
||||
int min_cnt; // min number of minimizers on each chain
|
||||
int min_chain_score; // min chaining score
|
||||
|
||||
float flt_max_dv;
|
||||
int flt_min_blen;
|
||||
|
||||
float mask_level;
|
||||
float pri_ratio;
|
||||
int best_n; // top best_n chains are subjected to DP alignment
|
||||
|
||||
@@ -59,7 +59,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
|
||||
|
||||
void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
|
||||
|
||||
int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
|
||||
void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
|
||||
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
|
||||
void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int rep_len);
|
||||
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
#include <stdio.h>
|
||||
#include <limits.h>
|
||||
#include "mmpriv.h"
|
||||
|
||||
void mm_idxopt_init(mm_idxopt_t *opt)
|
||||
@@ -8,6 +9,7 @@ void mm_idxopt_init(mm_idxopt_t *opt)
|
||||
opt->bucket_bits = 14;
|
||||
opt->mini_batch_size = 50000000;
|
||||
opt->batch_size = 4000000000ULL;
|
||||
opt->min_occ = 0, opt->max_occ = INT_MAX;
|
||||
}
|
||||
|
||||
void mm_mapopt_init(mm_mapopt_t *opt)
|
||||
@@ -25,6 +27,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
|
||||
opt->max_chain_skip = 25;
|
||||
opt->max_chain_iter = 5000;
|
||||
|
||||
opt->flt_max_dv = 1.0f;
|
||||
opt->flt_min_blen = 0;
|
||||
|
||||
opt->mask_level = 0.5f;
|
||||
opt->pri_ratio = 0.8f;
|
||||
opt->best_n = 5;
|
||||
|
||||
Reference in New Issue
Block a user