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working with toy examples

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This commit is contained in:
Heng Li
2018-07-15 10:55:00 -04:00
parent 951c0d1d35
commit 4b707aac92
5 changed files with 49 additions and 34 deletions
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splitidx.c
+15 -22
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@@ -26,17 +26,13 @@ FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
return fp;
}
FILE **mm_split_merge_prep(const char *prefix, int n_splits, mm_idx_t **mi_)
mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part)
{
mm_idx_t *mi = 0;
FILE **fp;
char *fn;
int i, j;
uint32_t m_seq = 0;
if (n_splits < 1) return 0;
*mi_ = 0;
fp = (FILE**)calloc(n_splits, sizeof(FILE*));
fn = (char*)calloc(strlen(prefix) + 10, 1);
for (i = 0; i < n_splits; ++i) {
sprintf(fn, "%s.%.4d.tmp", prefix, i);
@@ -45,31 +41,28 @@ FILE **mm_split_merge_prep(const char *prefix, int n_splits, mm_idx_t **mi_)
fprintf(stderr, "ERROR: failed to open temporary file '%s'\n", fn);
for (j = 0; j < i; ++j)
fclose(fp[j]);
free(fp);
free(fn);
return 0;
}
}
free(fn);
mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
for (i = 0; i < n_splits; ++i) {
uint32_t k, n;
mm_err_fread(&k, 4, 1, fp[i]);
mm_err_fread(&n, 4, 1, fp[i]);
mi->k = k;
if (mi->n_seq + n > m_seq) {
m_seq = mi->n_seq + n;
kroundup32(m_seq);
mi->seq = (mm_idx_seq_t*)realloc(mi->seq, sizeof(mm_idx_seq_t) * m_seq);
}
for (k = 0; k < n; ++i) {
mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same
mm_err_fread(&n_seq_part[i], 4, 1, fp[i]);
mi->n_seq += n_seq_part[i];
}
mi->seq = CALLOC(mm_idx_seq_t, mi->n_seq);
for (i = j = 0; i < n_splits; ++i) {
uint32_t k;
for (k = 0; k < n_seq_part[i]; ++k, ++j) {
uint8_t l;
mm_err_fread(&l, 1, 1, fp[i]);
mi->seq[mi->n_seq].name = (char*)calloc(l + 1, 1);
mm_err_fread(mi->seq[mi->n_seq].name, 1, l, fp[i]);
mm_err_fread(&mi->seq[mi->n_seq].len, 4, 1, fp[i]);
++mi->n_seq;
mi->seq[j].name = (char*)calloc(l + 1, 1);
mm_err_fread(mi->seq[j].name, 1, l, fp[i]);
mm_err_fread(&mi->seq[j].len, 4, 1, fp[i]);
}
}
*mi_ = mi;
return fp;
return mi;
}