query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
// do alignment; this takes most of computing time for indel calling
sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query + qbeg, qend - qbeg, &ap);
+ (uint8_t*)query, qend - qbeg, &ap);
score[K*n_types + t] = -sc;
/*
for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
fputc('\n', stderr);
- for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[qbeg + l]], stderr);
+ for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
fputc('\n', stderr);
- fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
+ fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
*/
}
}