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sa.c
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sa.c
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#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <stdio.h>
#include "fermi2.h"
#include "kvec.h"
static void sa_gen1(const rld_t *e, fmsa_t *sa, int64_t k, uint64_v *buf)
{
int c, mask = (1<<sa->ss) - 1;
uint64_t ok[e->asize1], k0 = k, l = 0;
size_t i;
buf->n = 0;
do {
++l;
c = rld_rank1a(e, k + 1, ok);
k = e->cnt[c] + ok[c] - 1;
if (c) {
if (((k - e->mcnt[1]) & mask) == 0) {
int64_t x = (k - e->mcnt[1]) >> sa->ss;
sa->ssa[x] = l;
kv_push(uint64_t, *buf, 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 {
const rld_t *e;
fmsa_t *sa;
uint64_v *buf;
} worker_t;
static void worker(void *data, long i, int tid)
{
worker_t *w = (worker_t*)data;
sa_gen1(w->e, w->sa, i, &w->buf[tid]);
}
fmsa_t *fm_sa_gen(const rld_t *e, int ssa_shift, int n_threads)
{
extern void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
fmsa_t *sa;
worker_t *w;
int i;
sa = calloc(1, sizeof(fmsa_t));
sa->ss = ssa_shift;
sa->m = e->mcnt[1];
for (sa->ms = 1; 1LL<<sa->ms < sa->m; ++sa->ms);
sa->n_ssa = (e->mcnt[0] - e->mcnt[1] + (1<<sa->ss) - 1) >> sa->ss;
sa->r2i = calloc(sa->m, 8);
sa->ssa = calloc(sa->n_ssa, 8);
w = calloc(1, sizeof(worker_t));
w->buf = calloc(n_threads, sizeof(uint64_v));
w->sa = sa;
w->e = e;
kt_for(n_threads, worker, w, sa->m);
for (i = 0; i < n_threads; ++i) free(w->buf[i].a);
free(w->buf); free(w);
return sa;
}
void fm_sa_destroy(fmsa_t *sa)
{
free(sa->r2i); free(sa->ssa); free(sa);
}
int64_t fm_sa(const rld_t *e, const fmsa_t *sa, int64_t k, int64_t *si)
{
int c, mask = (1<<sa->ss) - 1;
int64_t x = 0;
uint64_t ok[e->asize1];
*si = -1;
if (k >= e->mcnt[0]) return -1;
while (k < e->mcnt[1] || ((k - e->mcnt[1]) & mask)) {
++x;
c = rld_rank1a(e, k + 1, ok);
k = e->cnt[c] + ok[c] - 1;
if (c == 0) {
*si = sa->r2i[k];
return x - 1;
}
}
k = (k - e->mcnt[1]) >> sa->ss;
*si = sa->ssa[k] & ((1ULL<<sa->ms) - 1);
return x + (sa->ssa[k] >> sa->ms);
}
int fm_sa_dump(const fmsa_t *sa, const char *fn)
{
uint32_t y;
FILE *fp;
fp = fn && strcmp(fn, "-")? fopen(fn, "wb") : fdopen(fileno(stdout), "wb");
if (fp == 0) return -1;
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;
}
fmsa_t *fm_sa_restore(const char *fn)
{
FILE *fp;
uint32_t y;
fmsa_t *sa;
fp = fn && strcmp(fn, "-")? fopen(fn, "rb") : fdopen(fileno(stdin), "rb");
if (fp == 0) return 0;
sa = calloc(1, sizeof(fmsa_t));
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 = calloc(sa->m, 8);
sa->ssa = calloc(sa->n_ssa, 8);
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_sa(int argc, char *argv[])
{
int c, n_threads = 1, ssa_shift = 6;
fmsa_t *sa;
rld_t *e;
char *fn = 0;
while ((c = getopt(argc, argv, "t:s:o:")) >= 0) {
if (c == 't') n_threads = atoi(optarg);
else if (c == 's') ssa_shift = atoi(optarg);
else if (c == 'o') fn = optarg;
}
if (argc == optind) {
fprintf(stderr, "Usage: fermi2 sa [-t nThreads=%d] [-s stepShift=%d] <in.fmd>\n", n_threads, ssa_shift);
return 1;
}
e = rld_restore(argv[optind]);
if (e == 0) {
fprintf(stderr, "[E::%s] failed to load the FM-index\n", __func__);
return 1;
}
sa = fm_sa_gen(e, ssa_shift, n_threads);
//{int64_t i;for (i = 0; i < sa->n_ssa; ++i) fprintf(stderr, "S(%lld)=%lld\n", (i<<sa->ss) + e->mcnt[1], sa->ssa[i]>>sa->ms);}
fm_sa_dump(sa, fn);
rld_destroy(e);
fm_sa_destroy(sa);
return 0;
}