Package org.broadinstitute.gatk.engine.refdata.tracks

Examples of org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder

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    private List<ReferenceOrderedDataSource> getReferenceOrderedDataSources(final Collection<RMDTriplet> referenceMetaDataFiles,
                                                                            final SAMSequenceDictionary sequenceDictionary,
                                                                            final GenomeLocParser genomeLocParser,
                                                                            final ValidationExclusion.TYPE validationExclusionType,
                                                                            final Map<String, String> sampleRenameMap) {
        final RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser, validationExclusionType,
                                                            getArguments().disableAutoIndexCreationAndLockingWhenReadingRods,
                                                            sampleRenameMap);

        final List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
        for (RMDTriplet fileDescriptor : referenceMetaDataFiles)
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        return "UNKNOWN";

    }

    private LocationAwareSeekableRODIterator initializeRefSeq() {
        RMDTrackBuilder builder = new RMDTrackBuilder(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),
                                                      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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        if ( dbsnpIterator == null ) {

            if ( dbsnp == null )
                throw new UserException.BadInput("No dbSNP rod was provided, but one is needed to decipher the correct indel alleles from the HapMap records");

            RMDTrackBuilder builder = new RMDTrackBuilder(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),
                                                          getToolkit().getGenomeLocParser(),
                                                          getToolkit().getArguments().unsafe,
                                                          getToolkit().getArguments().disableAutoIndexCreationAndLockingWhenReadingRods,
                                                          null);
            dbsnpIterator = builder.createInstanceOfTrack(VCFCodec.class, new File(dbsnp.dbsnp.getSource())).getIterator();
            // Note that we should really use some sort of seekable iterator here so that the search doesn't take forever
            // (but it's complicated because the hapmap location doesn't match the dbsnp location, so we don't know where to seek to)
        }

        while ( dbsnpIterator.hasNext() ) {
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    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq);
        // disable auto-index creation/locking in the RMDTrackBuilder for tests
        builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
    }
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    public void setUp() {
        String fileName = privateTestDir + "TabularDataTest.dat";

        triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
        // disable auto-index creation/locking in the RMDTrackBuilder for tests
        builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
    }
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Related Classes of org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder

  • htsjdk.samtools.SAMSequenceDictionary
  • htsjdk.tribble.AbstractFeatureReader
  • htsjdk.tribble.index.Index
  • htsjdk.tribble.util.LittleEndianOutputStream
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet
  • org.broadinstitute.gatk.tools.walkers.coverage.DepthOfCoverage
  • org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF
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