Hierarchy For All Packages

Package Hierarchies:

• hadoop.org.apache.hadoop.mapreduce.lib.output,
• hadoop.org.apache.hadoop.mapreduce.lib.partition,
• org.seqdoop.hadoop_bam,
• org.seqdoop.hadoop_bam.cli,
• org.seqdoop.hadoop_bam.cli.plugins,
• org.seqdoop.hadoop_bam.cli.plugins.chipster,
• org.seqdoop.hadoop_bam.custom.jargs.gnu,
• org.seqdoop.hadoop_bam.util

Class Hierarchy

• java.lang.Object
  • org.seqdoop.hadoop_bam.BAMSplitGuesser
  • org.seqdoop.hadoop_bam.BCFSplitGuesser
  • org.seqdoop.hadoop_bam.util.BGZFBlockIndex
  • org.seqdoop.hadoop_bam.util.BGZFBlockIndexer
  • org.seqdoop.hadoop_bam.util.BGZFSplitGuesser
  • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
  • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
    • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.BooleanOption
    • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.DoubleOption
    • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.IntegerOption
    • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.LongOption
    • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption
  • org.seqdoop.hadoop_bam.util.ConfHelper
  • org.apache.hadoop.conf.Configured (implements org.apache.hadoop.conf.Configurable)
    • org.seqdoop.hadoop_bam.cli.CLIPlugin
      • org.seqdoop.hadoop_bam.cli.plugins.Cat
      • org.seqdoop.hadoop_bam.cli.CLIMRPlugin
        • org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin
          • org.seqdoop.hadoop_bam.cli.plugins.FixMate
          • org.seqdoop.hadoop_bam.cli.plugins.Sort
        • org.seqdoop.hadoop_bam.cli.plugins.chipster.Summarize
        • org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarySort
        • org.seqdoop.hadoop_bam.cli.plugins.VCFSort
      • org.seqdoop.hadoop_bam.cli.plugins.Index
      • org.seqdoop.hadoop_bam.cli.plugins.View
    • hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler<K,V> (implements org.apache.hadoop.util.Tool)
  • org.seqdoop.hadoop_bam.FormatConstants
  • org.seqdoop.hadoop_bam.cli.Frontend
  • htsjdk.variant.variantcontext.GenotypesContext (implements java.util.List<E>, java.io.Serializable)
    • htsjdk.variant.variantcontext.LazyGenotypesContext
      • org.seqdoop.hadoop_bam.LazyParsingGenotypesContext
        • org.seqdoop.hadoop_bam.LazyBCFGenotypesContext
        • org.seqdoop.hadoop_bam.LazyVCFGenotypesContext
  • org.seqdoop.hadoop_bam.util.GetSortedBAMHeader
  • org.apache.hadoop.mapreduce.InputFormat<K,V>
    • org.apache.hadoop.mapreduce.lib.input.FileInputFormat<K,V>
      • org.seqdoop.hadoop_bam.AnySAMInputFormat
      • org.seqdoop.hadoop_bam.BAMInputFormat
      • org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat<K,V>
      • org.seqdoop.hadoop_bam.CRAMInputFormat
      • org.seqdoop.hadoop_bam.FastaInputFormat
      • org.seqdoop.hadoop_bam.FastqInputFormat
      • org.seqdoop.hadoop_bam.QseqInputFormat
      • org.seqdoop.hadoop_bam.SAMInputFormat
      • org.seqdoop.hadoop_bam.VCFInputFormat
  • hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.IntervalSampler<K,V> (implements hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.Sampler<K,V>)
  • hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.RandomSampler<K,V> (implements hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.Sampler<K,V>)
  • hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.SplitSampler<K,V> (implements hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.Sampler<K,V>)
  • org.apache.hadoop.mapreduce.InputSplit
    • org.seqdoop.hadoop_bam.FileVirtualSplit (implements org.apache.hadoop.io.Writable)
  • java.io.InputStream (implements java.io.Closeable)
    • org.seqdoop.hadoop_bam.util.DataInputWrapper
    • htsjdk.samtools.seekablestream.SeekableStream
      • org.seqdoop.hadoop_bam.util.SeekableArrayStream
      • org.seqdoop.hadoop_bam.util.WrapSeekable<S>
  • org.seqdoop.hadoop_bam.LazyBAMRecordFactory (implements htsjdk.samtools.SAMRecordFactory)
  • org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache (implements org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.HeaderDataCache)
  • org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.Parser (implements htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser)
    • org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.Parser
    • org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.Parser
  • org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.HeaderDataCache (implements org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.HeaderDataCache)
  • org.seqdoop.hadoop_bam.LineReader
  • hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs<KEYOUT,VALUEOUT>
  • org.seqdoop.hadoop_bam.util.MurmurHash3
  • org.apache.hadoop.mapreduce.OutputFormat<K,V>
    • org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,V>
      • org.seqdoop.hadoop_bam.AnySAMOutputFormat<K>
        • org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat<K>
      • org.seqdoop.hadoop_bam.BAMOutputFormat<K>
        • org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat<K>
      • org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat<K>
      • org.seqdoop.hadoop_bam.CRAMOutputFormat<K>
        • org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat<K>
      • org.apache.hadoop.mapreduce.lib.output.TextOutputFormat<K,V>
        • org.seqdoop.hadoop_bam.FastqOutputFormat
        • org.seqdoop.hadoop_bam.QseqOutputFormat
      • org.seqdoop.hadoop_bam.VCFOutputFormat<K>
        • org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<K>
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • org.seqdoop.hadoop_bam.util.DataOutputWrapper
  • org.seqdoop.hadoop_bam.util.Pair<A,B>
  • org.apache.hadoop.mapreduce.Partitioner<KEY,VALUE>
    • hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner<K,V> (implements org.apache.hadoop.conf.Configurable)
  • org.apache.hadoop.mapreduce.RecordReader<KEYIN,VALUEIN> (implements java.io.Closeable)
    • org.seqdoop.hadoop_bam.BAMRecordReader
    • org.seqdoop.hadoop_bam.BCFRecordReader
    • org.seqdoop.hadoop_bam.CRAMRecordReader
    • org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
    • org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader
    • org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
    • org.seqdoop.hadoop_bam.SAMRecordReader
    • org.seqdoop.hadoop_bam.VCFRecordReader
  • org.apache.hadoop.mapreduce.RecordWriter<K,V>
    • org.seqdoop.hadoop_bam.BAMRecordWriter<K>
      • org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter<K>
    • org.seqdoop.hadoop_bam.BCFRecordWriter<K>
      • org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter<K>
    • org.seqdoop.hadoop_bam.CRAMRecordWriter<K>
      • org.seqdoop.hadoop_bam.KeyIgnoringCRAMRecordWriter<K>
    • org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
    • org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
    • org.seqdoop.hadoop_bam.SAMRecordWriter<K>
      • org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter<K>
    • org.seqdoop.hadoop_bam.VCFRecordWriter<K>
      • org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter<K>
  • org.seqdoop.hadoop_bam.ReferenceFragment (implements org.apache.hadoop.io.Writable)
  • org.seqdoop.hadoop_bam.util.SAMHeaderReader
  • org.seqdoop.hadoop_bam.util.SAMOutputPreparer
  • org.seqdoop.hadoop_bam.SAMRecordWritable (implements org.apache.hadoop.io.Writable)
  • org.seqdoop.hadoop_bam.SequencedFragment (implements org.apache.hadoop.io.Writable)
  • org.seqdoop.hadoop_bam.SplittingBAMIndex
  • org.seqdoop.hadoop_bam.SplittingBAMIndexer
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.OptionException
        • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.IllegalOptionValueException
        • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.UnknownOptionException
          • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.NotFlagException
          • org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.UnknownSuboptionException
      • java.lang.RuntimeException
        • org.seqdoop.hadoop_bam.FormatException
  • org.seqdoop.hadoop_bam.util.Timer
  • org.seqdoop.hadoop_bam.cli.Utils
  • htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, java.io.Serializable)
    • org.seqdoop.hadoop_bam.VariantContextWithHeader
  • org.seqdoop.hadoop_bam.VariantContextCodec
  • org.seqdoop.hadoop_bam.VariantContextWritable (implements org.apache.hadoop.io.Writable)
  • org.seqdoop.hadoop_bam.util.VCFHeaderReader

Interface Hierarchy

• hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.Sampler<K,V>
• org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.HeaderDataCache

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.seqdoop.hadoop_bam.FormatConstants.BaseQualityEncoding
    • org.seqdoop.hadoop_bam.SAMFormat
    • org.seqdoop.hadoop_bam.VCFFormat