Package org.broadinstitute.gatk.engine.iterators

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

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    private final LocusIteratorByState libs;

    public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, GATKSAMIterator iterator, List<GenomeLoc> intervals, Collection<String> sampleNames) {
        this.sourceInfo = shard.getReadProperties();
        this.readIterator = new GATKSAMRecordIterator(iterator);

        this.libs = new LocusIteratorByState(readIterator,sourceInfo,genomeLocParser,sampleNames);
        this.sourceIterator = new PeekableIterator<AlignmentContext>(libs);

        this.intervalIterator = intervals.size()>0 ? new PeekableIterator<GenomeLoc>(intervals.iterator()) : null;
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        else {
            final GenomeLoc loc = genomeLocParser.parseGenomeLoc(location);
            rawIterator = reader.query(loc.getContig(), loc.getStart(), loc.getStop(), false);
        }

        final GATKSAMRecordIterator iterator = new GATKSAMRecordIterator(rawIterator);

        final Set<String> samples = new HashSet<String>();
        for ( final SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups() )
            samples.add(rg.getSample());
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     *
     * @param reader a non-null reader
     * @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
     */
    public LocusIteratorByState(final SAMFileReader reader, final CloseableIterator<SAMRecord> it) {
        this(new GATKSAMRecordIterator(it),
                new LIBSDownsamplingInfo(false, 0),
                true,
                new GenomeLocParser(reader.getFileHeader().getSequenceDictionary()),
                SampleUtils.getSAMFileSamples(reader.getFileHeader()),
                false);
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Related Classes of org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator

  • org.broadinstitute.gatk.engine.executive.WindowMaker
  • org.broadinstitute.gatk.utils.locusiterator.LIBSPerformance
  • org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState
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