Package org.broadinstitute.gatk.engine.datasources.providers

Examples of org.broadinstitute.gatk.engine.datasources.providers.ReadView

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     * @return the result type T, the product of all the reduce calls
     */
    public T traverse(DuplicateWalker<M, T> walker,
                      ReadShardDataProvider dataProvider,
                      T sum) {
        PushbackIterator<SAMRecord> iter = new PushbackIterator<SAMRecord>(new ReadView(dataProvider).iterator());

        /**
         * while we still have more reads:
         * ok, here's the idea.  We get all the reads that start at the same position in the genome
         * We then split the list of reads into sublists of reads:
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        logger.debug(String.format("TraverseReadsPairs.traverse Covered dataset is %s", dataProvider));

        if( !dataProvider.hasReads() )
            throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");

        ReadView reads = new ReadView(dataProvider);
        List<SAMRecord> pairs = new ArrayList<SAMRecord>();

        boolean done = walker.isDone();
        for(SAMRecord read: reads) {
            if ( done ) break;
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    }


    private Iterator<MapData> makeDataIterator(final ReadShardDataProvider dataProvider) {
        return new Iterator<MapData> ()  {
            final ReadView reads = new ReadView(dataProvider);
            final ReadReferenceView reference = new ReadReferenceView(dataProvider);
            final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
            final Iterator<SAMRecord> readIterator = reads.iterator();

            @Override public boolean hasNext() { return ! engine.exceedsRuntimeLimit() && readIterator.hasNext(); }

            @Override
            public MapData next() {
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Related Classes of org.broadinstitute.gatk.engine.datasources.providers.ReadView

  • org.broadinstitute.gatk.engine.traversals.TraverseDuplicates
  • org.broadinstitute.gatk.engine.traversals.TraverseReadPairs
  • org.broadinstitute.gatk.engine.traversals.TraverseReadsNano
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