}
public void UpdatePositionMetrics (PositionInfo p, char reference_nucleotide) {
Iterator<MappedBaseInfo> i = p.mappedBases.iterator();
while (i.hasNext()) {
MappedBaseInfo b = i.next();
if (b.nucleotide != reference_nucleotide) {
mismatch_total++;
String mismatch_lookup = "";
mismatch_lookup += reference_nucleotide;