const void *rghash)
{
extern void ks_introsort_uint32_t(int, uint32_t*);
- int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2;
+ int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query;
khash_t(rg) *hash = (khash_t(rg)*)rghash;
free(inscns_aux);
}
// compute the likelihood given each type of indel for each read
- ref2 = calloc(right - left + max_ins + 2, 1);
+ max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+ ref2 = calloc(max_ref2, 1);
query = calloc(right - left + max_rd_len + max_ins + 2, 1);
score1 = calloc(N * n_types, sizeof(int));
score2 = calloc(N * n_types, sizeof(int));
}
for (; j < right && ref[j]; ++j)
ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
+ for (; k < max_ref2; ++k) ref2[k] = 4;
if (j < right) right = j;
// align each read to ref2
for (s = K = 0; s < n; ++s) {
const uint8_t *qual = bam1_qual(p->b), *bq;
uint8_t *qq;
qq = calloc(qend - qbeg, 1);
- bq = (uint8_t*)bam_aux_get(p->b, "BQ");
+ bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
if (bq) ++bq; // skip type
for (l = qbeg; l < qend; ++l) {
- qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
+ qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
}