Examples of org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator

     *
     * @param loc
     */
    protected void validateLocation( GenomeLoc loc ) {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(loc));
        GenomeLocusIterator shardIterator = new GenomeLocusIterator(genomeLocParser,loc);


        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, loc, null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);


        while (shardIterator.hasNext()) {
            GenomeLoc locus = shardIterator.next();


            ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
            char expected = Character.toUpperCase(StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0));
            char actual = view.getReferenceContext(locus).getBaseAsChar();

     * @param provider
     */
    public AllLocusView(LocusShardDataProvider provider) {
        super(provider);
        // Seed the state tracking members with the first possible seek position and the first possible locus context.
        locusIterator = new GenomeLocusIterator(genomeLocParser, provider.getLocus());
    }

Related Classes of org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator

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