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r1269: added --write-junc

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in preparation for 2-pass
This commit is contained in:
Heng Li
2025-04-11 01:00:15 -04:00
parent bd03d975fc
commit a5411fc3c0
5 changed files with 59 additions and 2 deletions
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map.c
+8 -1
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@@ -594,9 +594,16 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_err_fwrite(r->p, r->p->capacity, 4, p->fp_split);
}
}
} else if (p->opt->flag & MM_F_OUT_JUNC) { // extra logic for --write-junc
for (j = 0; j < s->n_reg[i]; ++j) {
const mm_reg1_t *r = &s->reg[i][j];
if (r->id != r->parent) continue;
mm_write_junc(&p->str, mi, t, r);
if (p->str.l > 0) mm_err_puts(p->str.s);
}
} else if (s->n_reg[i] > 0) { // the query has at least one hit
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
const mm_reg1_t *r = &s->reg[i][j];
assert(!r->sam_pri || r->id == r->parent);
if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
continue;