Package org.broad.igv.util

Examples of org.broad.igv.util.CompressionUtils

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public class BedToPeaks {
    private static Map<String, String> colorMap;
    private static CompressionUtils compressionUtils;

    public BedToPeaks() {
        compressionUtils = new CompressionUtils();
    }
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    private final CompressionUtils compressionUtils;

    public PeakParser(String path) throws IOException {
        this.path = path;
        loadHeader();
        compressionUtils = new CompressionUtils();
    }
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            fis.readFully(buffer);

            // decompress if necessary - the buffer size is 0 for uncomressed data
            // Note:  BBFile Table C specifies a decompression buffer size
            if (uncompressBufSize > 0)
                zoomBuffer = (new CompressionUtils()).decompress(buffer, uncompressBufSize);
            else
                zoomBuffer = buffer;    // use uncompressed read buffer directly

        } catch (IOException ex) {
            log.error("Error reading Zoom level " + this.zoomLevel + " data for leaf item ",  ex);
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            fis.readFully(buffer);

            // decompress if necessary - the buffer size is 0 for uncompressed data
            // Note:  BBFile Table C specifies a decompression buffer size
            if(uncompressBufSize > 0)
                wigBuffer = (new CompressionUtils()).decompress(buffer, uncompressBufSize);
            else
                wigBuffer = buffer;    // use uncompressed read buffer directly
        }catch(IOException ex) {
            log.error("Error reading Wig section for leaf item ", ex);
            String error = String.format("Error reading Wig section for leaf item %d\n");
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        } catch (IOException ex) {
            log.error("Error opening output stream to file: " + file, ex);
            throw new DataLoadException("Error creating file", "" + file);
        }

        compressionUtils = new CompressionUtils();
    }
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            fis.readFully(buffer);

            // decompress if necessary - the buffer size is 0 for uncompressed data
            // Note:  BBFile Table C specifies a decompression buffer size
            if (uncompressBufSize > 0)
                bedBuffer = (new CompressionUtils()).decompress(buffer, uncompressBufSize);
            else
                bedBuffer = buffer;    // use uncompressed read buffer directly

        } catch (IOException ex) {
            String error = String.format("Error reading Bed data for leaf item %d \n");
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        BufferedReader br = null;
        fos = null;
        currentChr = null;
        currentChrBuffer = null;
        chrPositionMap = new HashMap<String, IndexEntry>();
        compressionUtils = new CompressionUtils();
        EQTLCodec codec = new EQTLCodec(null);

        try {
            fos = new FileOutputStream(outputFile);
            writeHeader();
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        } catch (IOException ex) {
            log.error("Error loading file: " + locator.getPath(), ex);
            throw new DataLoadException("Error loading file: " + ex.toString(), locator.getPath());
        }
        compressionUtils = new CompressionUtils();
    }
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Related Classes of org.broad.igv.util.CompressionUtils

  • org.broad.igv.bbfile.BigBedDataBlock
  • org.broad.igv.bbfile.BigWigDataBlock
  • org.broad.igv.bbfile.ZoomDataBlock
  • org.broad.igv.gwas.EqtlPreprocessor
  • org.broad.igv.peaks.BedToPeaks
  • org.broad.igv.peaks.PeakParser
  • org.broad.igv.tdf.TDFReader
  • org.broad.igv.tdf.TDFWriter
  • java.util.zip.Deflater
  • java.util.zip.Inflater
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