private ReferenceOrderedView getReferenceOrderedView(
final ActiveRegionWalker<M, T> walker,
final LocusShardDataProvider dataProvider,
final LocusView locusView) {
if (WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE_ORDERED_DATA)
return new ManagingReferenceOrderedView(dataProvider);
else return (RodLocusView) locusView;
}
/**
* Gets the best view of loci for this walker given the available data.
*
* @param walker walker to interrogate.
* @param dataProvider Data which which to drive the locus view.
* @return A view of the locus data, where one iteration of the locus view maps to one iteration
* of the traversal.
*/
private LocusView getLocusView(
final Walker<M, T> walker, final LocusShardDataProvider dataProvider) {
final DataSource dataSource = WalkerManager.getWalkerDataSource(walker);
if (dataSource == DataSource.READS) return new CoveredLocusView(dataProvider);
else if (dataSource
== DataSource
.REFERENCE) // || ! GenomeAnalysisEngine.instance.getArguments().enableRodWalkers )
return new AllLocusView(dataProvider);
else if (dataSource == DataSource.REFERENCE_ORDERED_DATA) return new RodLocusView(dataProvider);
else throw new UnsupportedOperationException("Unsupported traversal type: " + dataSource);
}