Hierarchy For All Packages

Package Hierarchies:

uk.ac.sanger.npg.bam.util, uk.ac.sanger.npg.illumina, uk.ac.sanger.npg.illumina.file.reader, uk.ac.sanger.npg.picard

Class Hierarchy

• java.lang.Object
  • uk.ac.sanger.npg.picard.AlignmentFilterMetric
  • uk.ac.sanger.npg.picard.AlignmentFilterMetric.SQ
  • uk.ac.sanger.npg.bam.util.BamUtils
  • net.sf.picard.cmdline.CommandLineProgram
    • uk.ac.sanger.npg.picard.PicardCommandLine
      • uk.ac.sanger.npg.picard.AlignmentFilter
      • uk.ac.sanger.npg.picard.BamIndexDecoder
      • uk.ac.sanger.npg.picard.BamMerger
      • uk.ac.sanger.npg.picard.BamQualityQuantisation
      • uk.ac.sanger.npg.picard.BamReadTrimmer
      • uk.ac.sanger.npg.picard.BamTagStripper
      • uk.ac.sanger.npg.picard.ChangeBamHeader
      • uk.ac.sanger.npg.illumina.Illumina2bam
      • uk.ac.sanger.npg.picard.SplitBamByReadGroup
  • uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader (implements java.io.Closeable, java.util.Iterator<E>)
    • uk.ac.sanger.npg.illumina.file.reader.BCLFileReader
    • uk.ac.sanger.npg.illumina.file.reader.FilterFileReader
    • uk.ac.sanger.npg.illumina.file.reader.PositionFileReader
      • uk.ac.sanger.npg.illumina.file.reader.CLocsFileReader
      • uk.ac.sanger.npg.illumina.file.reader.LocsFileReader
      • uk.ac.sanger.npg.illumina.file.reader.PosFileReader
    • uk.ac.sanger.npg.illumina.file.reader.SCLFileReader
  • uk.ac.sanger.npg.picard.IndexDecoder
  • uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMatch
  • uk.ac.sanger.npg.picard.IndexDecoder.NamedBarcode
  • uk.ac.sanger.npg.illumina.Lane
  • net.sf.picard.metrics.MetricBase
    • uk.ac.sanger.npg.picard.IndexDecoder.BarcodeMetric
  • uk.ac.sanger.npg.illumina.file.reader.PositionFileReader.Position
  • uk.ac.sanger.npg.illumina.Tile