bca->indelreg = 0;
for (t = 0; t < n_types; ++t) {
int l, ir;
- ka_param2_t ap = ka_param2_qual;
- ap.band_width = abs(types[t]) + 3;
+ kpa_par_t ap = { 1e-4, 1e-2, 10 };
+ ap.bw = abs(types[t]) + 3;
// compute indelreg
if (types[t] == 0) ir = 0;
else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
bam_pileup1_t *p = plp[s] + i;
int qbeg, qend, tbeg, tend, sc;
uint8_t *seq = bam1_seq(p->b);
+ // FIXME: the following skips soft clips, but using them may be more sensitive.
// determine the start and end of sequences for alignment
qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
// write the query sequence
for (l = qbeg; l < qend; ++l)
query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
- // do alignment; this takes most of computing time for indel calling
- if (0) {
- uint8_t *qq = calloc(qend - qbeg, 1);
- for (l = 0; l < qend - qbeg; ++l) qq[l] = 23;
+ { // do alignment; this is the bottleneck
+ const uint8_t *qual = bam1_qual(p->b), *bq;
+ uint8_t *qq = 0;
+ qq = calloc(qend - qbeg, 1);
+ bq = (uint8_t*)bam_aux_get(p->b, "BQ");
+ if (bq) ++bq;
+ for (l = qbeg; l < qend; ++l)
+ qq[l - qbeg] = bq? qual[l] + (bq[l] - 33) : qual[l];
sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, qq, &kpa_par_alt, 0, 0);
+ (uint8_t*)query, qend - qbeg, qq, &ap, 0, 0);
score[K*n_types + t] = sc;
- } else {
- sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, &ap);
- score[K*n_types + t] = -sc;
+ free(qq);
}
/*
for (l = 0; l < tend - tbeg + abs(types[t]); ++l)