Package org.broadinstitute.gatk.engine.datasources.providers

Examples of org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView



    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)
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