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1 #include <string.h>
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2 #include <stdio.h>
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3 #include <stdlib.h>
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4 #include "bwt.h"
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5 #include "utils.h"
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6
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7 void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
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8 {
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9 FILE *fp;
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10 fp = xopen(fn, "wb");
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11 fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
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12 fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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13 fwrite(bwt->bwt, sizeof(bwtint_t), bwt->bwt_size, fp);
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14 fclose(fp);
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15 }
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16
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17 void bwt_dump_sa(const char *fn, const bwt_t *bwt)
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18 {
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19 FILE *fp;
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20 fp = xopen(fn, "wb");
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21 fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
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22 fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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23 fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
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24 fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
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25 fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
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26 fclose(fp);
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27 }
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28
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29 void bwt_restore_sa(const char *fn, bwt_t *bwt)
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30 {
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31 char skipped[256];
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32 FILE *fp;
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33 bwtint_t primary;
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34
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35 fp = xopen(fn, "rb");
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36 fread(&primary, sizeof(bwtint_t), 1, fp);
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37 xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
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38 fread(skipped, sizeof(bwtint_t), 4, fp); // skip
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39 fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
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40 fread(&primary, sizeof(bwtint_t), 1, fp);
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41 xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
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42
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43 bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
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44 bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
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45 bwt->sa[0] = -1;
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46
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47 fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
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48 fclose(fp);
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49 }
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50
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51 bwt_t *bwt_restore_bwt(const char *fn)
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52 {
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53 bwt_t *bwt;
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54 FILE *fp;
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55
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56 bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
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57 fp = xopen(fn, "rb");
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58 fseek(fp, 0, SEEK_END);
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59 bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
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60 bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
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61 fseek(fp, 0, SEEK_SET);
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62 fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
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63 fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
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64 fread(bwt->bwt, 4, bwt->bwt_size, fp);
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65 bwt->seq_len = bwt->L2[4];
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66 fclose(fp);
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67 bwt_gen_cnt_table(bwt);
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68
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69 return bwt;
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70 }
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71
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72 void bwt_destroy(bwt_t *bwt)
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73 {
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74 if (bwt == 0) return;
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75 free(bwt->sa); free(bwt->bwt);
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76 free(bwt);
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77 }
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