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ssa.c
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ssa.c
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#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "rb3priv.h"
#include "fm-index.h"
#include "kalloc.h"
#include "kthread.h"
#include "ketopt.h"
typedef struct { size_t n, m; uint64_t *a; } uint64_v;
static void ssa_gen1(void *km, const rb3_fmi_t *f, rb3_ssa_t *sa, int64_t k, uint64_v *buf)
{
int32_t c, mask = (1<<sa->ss) - 1;
int64_t ok[RB3_ASIZE], k0 = k, l = 0;
size_t i;
buf->n = 0;
do {
++l;
c = rb3_fmi_rank1a(f, k, ok);
k = f->acc[c] + ok[c];
if (c) {
if (((k - f->acc[1]) & mask) == 0) {
int64_t x = (k - f->acc[1]) >> sa->ss;
assert(x < sa->n_ssa);
sa->ssa[x] = l;
Kgrow(km, uint64_t, buf->a, buf->n, buf->m);
buf->a[buf->n++] = x;
}
} else sa->r2i[k] = k0;
} while (c);
for (i = 0; i < buf->n; ++i)
sa->ssa[buf->a[i]] = (l - 1 - sa->ssa[buf->a[i]]) << sa->ms | k0;
}
typedef struct {
void **km;
const rb3_fmi_t *f;
rb3_ssa_t *sa;
uint64_v *buf;
} worker_t;
static void worker(void *data, long i, int tid)
{
worker_t *w = (worker_t*)data;
ssa_gen1(w->km[tid], w->f, w->sa, i, &w->buf[tid]);
}
rb3_ssa_t *rb3_ssa_gen(const rb3_fmi_t *f, int ssa_shift, int n_threads)
{
rb3_ssa_t *sa;
worker_t *w;
int i;
sa = RB3_CALLOC(rb3_ssa_t, 1);
sa->ss = ssa_shift;
sa->m = f->acc[1];
for (sa->ms = 1; 1LL<<sa->ms < sa->m; ++sa->ms) {}
sa->n_ssa = (f->acc[RB3_ASIZE] - f->acc[1] + (1LL<<sa->ss) - 1LL) >> sa->ss;
sa->r2i = RB3_CALLOC(uint64_t, sa->m);
sa->ssa = RB3_CALLOC(uint64_t, sa->n_ssa);
w = RB3_CALLOC(worker_t, 1);
w->km = RB3_CALLOC(void*, n_threads);
for (i = 0; i < n_threads; ++i)
w->km[i] = km_init();
w->buf = RB3_CALLOC(uint64_v, n_threads);
w->sa = sa, w->f = f;
kt_for(n_threads, worker, w, sa->m);
for (i = 0; i < n_threads; ++i)
km_destroy(w->km[i]);
free(w->km); free(w->buf); free(w);
return sa;
}
void rb3_ssa_destroy(rb3_ssa_t *sa)
{
if (sa == 0) return;
free(sa->r2i); free(sa->ssa); free(sa);
}
int64_t rb3_ssa(const rb3_fmi_t *f, const rb3_ssa_t *sa, int64_t k, int64_t *si)
{
int32_t c, mask = (1<<sa->ss) - 1;
int64_t x = 0;
int64_t ok[RB3_ASIZE];
*si = -1;
if (k >= f->acc[6]) return -1;
while (k < f->acc[1] || ((k - f->acc[1]) & mask)) {
++x;
c = rb3_fmi_rank1a(f, k, ok);
k = f->acc[c] + ok[c];
if (c == 0) {
*si = sa->r2i[k];
return x - 1;
}
}
k = (k - f->acc[1]) >> sa->ss;
*si = sa->ssa[k] & ((1ULL<<sa->ms) - 1);
return x + (sa->ssa[k] >> sa->ms);
}
int rb3_ssa_dump(const rb3_ssa_t *sa, const char *fn)
{
uint32_t y;
FILE *fp;
fp = fn && strcmp(fn, "-")? fopen(fn, "wb") : fdopen(1, "wb");
if (fp == 0) return -1;
fwrite("SSA\1", 1, 4, fp);
y = sa->ss; fwrite(&y, 4, 1, fp);
y = sa->ms; fwrite(&y, 4, 1, fp);
fwrite(&sa->m, 8, 1, fp);
fwrite(&sa->n_ssa, 8, 1, fp);
fwrite(sa->r2i, 8, sa->m, fp);
fwrite(sa->ssa, 8, sa->n_ssa, fp);
fclose(fp);
return 0;
}
rb3_ssa_t *rb3_ssa_restore(const char *fn)
{
FILE *fp;
uint32_t y;
char magic[4];
rb3_ssa_t *sa;
fp = fn && strcmp(fn, "-")? fopen(fn, "rb") : fdopen(0, "rb");
if (fp == 0) return 0;
fread(magic, 1, 4, fp);
if (strncmp(magic, "SSA\1", 4) != 0) return 0; // wrong magic
sa = RB3_CALLOC(rb3_ssa_t, 1);
fread(&y, 4, 1, fp); sa->ss = y;
fread(&y, 4, 1, fp); sa->ms = y;
fread(&sa->m, 8, 1, fp);
fread(&sa->n_ssa, 8, 1, fp);
sa->r2i = RB3_CALLOC(uint64_t, sa->m);
sa->ssa = RB3_CALLOC(uint64_t, sa->n_ssa);
if (sa->ssa == 0 || sa->r2i == 0) {
free(sa->r2i); free(sa->ssa); free(sa);
return 0;
}
fread(sa->r2i, 8, sa->m, fp);
fread(sa->ssa, 8, sa->n_ssa, fp);
fclose(fp);
return sa;
}
int main_ssa(int argc, char *argv[])
{
int c, n_threads = 4, ssa_shift = 8;
rb3_ssa_t *sa;
rb3_fmi_t f;
char *fn = 0;
ketopt_t o = KETOPT_INIT;
while ((c = ketopt(&o, argc, argv, 1, "t:s:o:", 0)) >= 0) {
if (c == 't') n_threads = atoi(o.arg);
else if (c == 's') ssa_shift = atoi(o.arg);
else if (c == 'o') fn = o.arg;
}
if (argc == o.ind) {
fprintf(stderr, "Usage: ropebwt3 ssa [options] <in.fmd>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
fprintf(stderr, " -s INT sample rate one SA per 2**INT bases [%d]\n", ssa_shift);
fprintf(stderr, " -o FILE output to file [stdout]\n");
return 1;
}
rb3_fmi_restore(&f, argv[o.ind], 0);
if (f.e == 0 && f.r == 0) {
fprintf(stderr, "[E::%s] failed to load the FM-index\n", __func__);
return 1;
}
sa = rb3_ssa_gen(&f, ssa_shift, n_threads);
rb3_ssa_dump(sa, fn);
rb3_fmi_free(&f);
rb3_ssa_destroy(sa);
return 0;
}