Package org.broadinstitute.gatk.engine.walkers

Examples of org.broadinstitute.gatk.engine.walkers.DataSource


     * @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( Walker<M,T> walker, 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 )
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