private Iterator<MapData> makeDataIterator(final ReadShardDataProvider dataProvider) {
return new Iterator<MapData> () {
final ReadView reads = new ReadView(dataProvider);
final ReadReferenceView reference = new ReadReferenceView(dataProvider);
final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
final Iterator<SAMRecord> readIterator = reads.iterator();
@Override public boolean hasNext() { return ! engine.exceedsRuntimeLimit() && readIterator.hasNext(); }
@Override
public MapData next() {
final SAMRecord read = readIterator.next();
final ReferenceContext refContext = ! read.getReadUnmappedFlag()
? reference.getReferenceContext(read)
: null;
// if the read is mapped, create a metadata tracker
final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
? rodView.getReferenceOrderedDataForRead(read)
: null;
// update the number of reads we've seen
dataProvider.getShard().getReadMetrics().incrementNumIterations();