Examples of RMDTrack

org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack
@author aaron
Class RMDTrack
the basics of what a reference metadata track must contain.

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

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

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

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

        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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