// To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
// check the number of N's in the sequence and skip places where half or more reference bases are Ns.
int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
- if ( nN*2>i ) { free(aux); return -1; }
+ if ( nN*2>(i-pos) ) { free(aux); return -1; }
ks_introsort(uint32_t, m, aux);
// squeeze out identical types