78 lines
1.9 KiB
C
78 lines
1.9 KiB
C
#include <string.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include "bwt.h"
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#include "utils.h"
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void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
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{
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FILE *fp;
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fp = xopen(fn, "wb");
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fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
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fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
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fclose(fp);
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}
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void bwt_dump_sa(const char *fn, const bwt_t *bwt)
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{
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FILE *fp;
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fp = xopen(fn, "wb");
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fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
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fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
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fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
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fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
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fclose(fp);
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}
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void bwt_restore_sa(const char *fn, bwt_t *bwt)
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{
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char skipped[256];
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FILE *fp;
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bwtint_t primary;
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fp = xopen(fn, "rb");
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fread(&primary, sizeof(bwtint_t), 1, fp);
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xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
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fread(skipped, sizeof(bwtint_t), 4, fp); // skip
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fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
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fread(&primary, sizeof(bwtint_t), 1, fp);
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xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
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bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
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bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
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bwt->sa[0] = -1;
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fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
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fclose(fp);
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}
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bwt_t *bwt_restore_bwt(const char *fn)
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{
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bwt_t *bwt;
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FILE *fp;
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bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
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fp = xopen(fn, "rb");
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fseek(fp, 0, SEEK_END);
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bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
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bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
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fseek(fp, 0, SEEK_SET);
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fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
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fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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fread(bwt->bwt, 4, bwt->bwt_size, fp);
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bwt->seq_len = bwt->L2[4];
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fclose(fp);
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bwt_gen_cnt_table(bwt);
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return bwt;
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}
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void bwt_destroy(bwt_t *bwt)
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{
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if (bwt == 0) return;
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free(bwt->sa); free(bwt->bwt);
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free(bwt);
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}
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