Package org.broad.igv.feature.tribble

Examples of org.broad.igv.feature.tribble.MUTCodec

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    public MUTSorter(File inputFile, File outputFile) {

        super(inputFile, outputFile);
        MUTCodec codec = new MUTCodec(inputFile.getAbsolutePath(), null);
        chrCol = codec.getChrColumn();
        startCol = codec.getStartColumn();
    }
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        return tracks;
    }


    private MUTCodec getCodec() {
        if (codec == null) codec = new MUTCodec(locator.getPath(), genome);
        return codec;
    }
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        AsciiLineReader reader = null;
        String nextLine = null;

        try {

            if (codec == null) codec = new MUTCodec(locator.getPath(), genome);

            Map<String, List<htsjdk.tribble.Feature>> mutationMap = new LinkedHashMap();

            reader = ParsingUtils.openAsciiReader(locator);
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Related Classes of org.broad.igv.feature.tribble.MUTCodec

  • htsjdk.tribble.readers.AsciiLineReader
  • htsjdk.tribble.readers.LineIterator
  • htsjdk.tribble.readers.LineIteratorImpl
  • org.broad.igv.feature.Mutation
  • org.broad.igv.feature.MutationTrackLoader
  • org.broad.igv.tools.sort.MUTSorter
  • org.broad.igv.util.collections.MultiMap
  • java.io.BufferedReader
  • org.broad.igv.exceptions.DataLoadException
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