Examples of org.broadinstitute.gatk.engine.refdata.SeekableRODIterator

Package org.broadinstitute.gatk.engine.refdata

Examples of org.broadinstitute.gatk.engine.refdata.SeekableRODIterator

org.broadinstitute.gatk.engine.refdata.SeekableRODIterator
Wrapper class for iterators over ROD objects. It is assumed that the underlying iterator can only perform standard next() operation, which advances it to the next ROD in the stream (i.e. reads the data file line by line). This iterator 1) shifts the focus from record-based traversal to position-based traversal, and 2) adds querying seekForward() method. Namely, this iterator's next() method advances not to the next ROD in the underlying stream, but to the next genomic position covered by (at least one) ROD, and returns all RODs overlapping with that position as a RODRecordList collection-like object. Similarly, when seekForward(interval) is called, this iterator skips all the RODs from the underlying stream, until it reaches specified genomic interval, and returns the list of all RODs overlapping with that interval. NOTE: this iterator has a STATE: next() operation is not allowed after a seekForward() to a non-point (extended) interval of length > 1. Such a call would leave the iterator in an inconsistent state. seekForward() can always be called after either seekForward() or next() (as long as usual ordering criteria are satisfied: the query interval location can neither start before the current position, nor end before the previous query end). seekForward to an interval of length 1 reenables next() operation. Created by IntelliJ IDEA. User: asivache Date: Sep 10, 2009 Time: 6:20:46 PM To change this template use File | Settings | File Templates.

     */
    public LocationAwareSeekableRODIterator createNewResource() {
        if(numIterators() > 0)
            throw new ReviewedGATKException("BUG: Tried to create multiple iterators over streaming ROD interface");
        RMDTrack track = builder.createInstanceOfTrack(fileDescriptor);
        LocationAwareSeekableRODIterator iter = new SeekableRODIterator(track.getHeader(),track.getSequenceDictionary(),referenceSequenceDictionary,genomeLocParser,track.getIterator());
        return (flashbackData) ? new FlashBackIterator(iter) : iter;
    }

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                                                      getToolkit().getGenomeLocParser(),
                                                      getToolkit().getArguments().unsafe,
                                                      getToolkit().getArguments().disableAutoIndexCreationAndLockingWhenReadingRods,
                                                      null);
        RMDTrack refseq = builder.createInstanceOfTrack(RefSeqCodec.class,refSeqGeneList);
        return new SeekableRODIterator(refseq.getHeader(),refseq.getSequenceDictionary(),getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),
                getToolkit().getGenomeLocParser(),refseq.getIterator());
    }

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    @Override
    protected LocationAwareSeekableRODIterator createIteratorFromResource(DataStreamSegment position, RMDTrack track) {
        try {
            if (position instanceof MappedStreamSegment) {
                GenomeLoc pos = ((MappedStreamSegment) position).locus;
                return new SeekableRODIterator(header,sequenceDictionary,referenceSequenceDictionary,genomeLocParser,track.query(pos));
            } else {
                return new SeekableRODIterator(header,sequenceDictionary,referenceSequenceDictionary,genomeLocParser,track.getIterator());
            }
        } catch (FileNotFoundException e) {
            throw new UserException.CouldNotReadInputFile(fileDescriptor.getName(), "it could not be found");
        } catch (IOException e) {
            throw new ReviewedGATKException("Unable to create iterator for rod named " + fileDescriptor.getName(),e);

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Related Classes of org.broadinstitute.gatk.engine.refdata.SeekableRODIterator

org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPool

org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool

org.broadinstitute.gatk.engine.refdata.utils.GATKFeature

org.broadinstitute.gatk.tools.walkers.coverage.DepthOfCoverage

org.broadinstitute.gatk.utils.GenomeLoc

org.broadinstitute.gatk.utils.exceptions.UserException

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

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