} catch (FileNotFoundException e) {
throw new StingException(String.format("Could not open file(s) for writing"));
}
}
public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
<BUG>Variation call1 = (Variation)tracker.lookup("callset1", null);
Variation call2 = (Variation)tracker.lookup("callset2", null);
if ( call1 == null && call2 == null )</BUG>
return;
printVariant(union_writer, call1 != null ? call1 : call2);

} catch (FileNotFoundException e) {
throw new StingException(String.format("Could not open file(s) for writing"));
}
}
public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
RODRecordList<ReferenceOrderedDatum> call1List = tracker.getTrackData("callset1", null);
RODRecordList<ReferenceOrderedDatum> call2List = tracker.getTrackData("callset2", null);
Variation call1 = (call1List == null ? null : (Variation)call1List.getRecords().get(0));
Variation call2 = (call2List == null ? null : (Variation)call2List.getRecords().get(0));
if ( call1 == null && call2 == null )
return;
printVariant(union_writer, call1 != null ? call1 : call2);
