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

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

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            featureReader = new TestFeatureReader(inputFile.getAbsolutePath(), codec);
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
        SAMSequenceDictionary sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);
        return new RMDTrack(descriptor.getCodecClass(), name, inputFile, featureReader, sequenceDictionary, genomeLocParser, codec);
    }
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     * @return The newly created resource.
     */
    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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        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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        super(referenceSequenceDictionary,genomeLocParser);
        this.fileDescriptor = fileDescriptor;
        this.builder = builder;

        // prepopulate one RMDTrack
        RMDTrack track = builder.createInstanceOfTrack(fileDescriptor);
        this.addNewResource(track);

        // Pull the proper header and sequence dictionary from the prepopulated track.
        this.header = track.getHeader();
        this.sequenceDictionary = track.getSequenceDictionary();
    }
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Related Classes of org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack

  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPool
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool
  • org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator
  • org.broadinstitute.gatk.engine.refdata.utils.TestRMDTrackBuilder
  • org.broadinstitute.gatk.tools.walkers.coverage.DepthOfCoverage
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