INNER CODE UNIT · C
nt_aa
lh3/miniprot · align.c:112
nt_aa = nt[i] > 3 || nt[i+1] > 3 || nt[i+2] > 3? aa_ambi : ns_tab_codon[codon];
aa_aa = ns_tab_aa20[(uint8_t)aa[j]];
s = opt->mat[nt_aa * opt->asize + aa_aa];
e->n_stop += (nt_aa == aa_stop);
e->n_iden += (nt_aa == aa_aa);
e->n_plus += (s > 0);
e->dp_max += s;
}
nl += len3, al += len, e->blen += len3;
} else if (op == NS_CIGAR_I) {
e->dp_max -= opt->go + opt->ge * len;
al += len, e->blen += len3;
} else if (op == NS_CIGAR_D) {
for (i = nl, l = 0; l < len; ++l, i += 3) { // we need to count in-frame stop codons in deletions
uint8_t codon = nt[i]<<4 | nt[i+1]<<2 | nt[i+2];
uint8_t nt_aa = nt[i] > 3 || nt[i+1] > 3 || nt[i+2] > 3? aa_ambi : ns_tab_codon[codon];
e->n_stop += (nt_aa == aa_stop);
}