Class Hierarchy (dsh-bio-tools 2.2 API)

Class Hierarchy

java.lang.Object
- org.dishevelled.bio.tools.About
- org.dishevelled.bio.tools.AbstractFilter (implements java.util.concurrent.Callable<V>)
  - org.dishevelled.bio.tools.FilterBed
  - org.dishevelled.bio.tools.FilterFasta
  - org.dishevelled.bio.tools.FilterFastq
  - org.dishevelled.bio.tools.FilterGaf
  - org.dishevelled.bio.tools.FilterGfa1
  - org.dishevelled.bio.tools.FilterGfa2
  - org.dishevelled.bio.tools.FilterGff3
  - org.dishevelled.bio.tools.FilterPaf
  - org.dishevelled.bio.tools.FilterRgfa
  - org.dishevelled.bio.tools.FilterSam
  - org.dishevelled.bio.tools.FilterVcf
- org.dishevelled.bio.tools.AbstractRenameReferences (implements java.util.concurrent.Callable<V>)
  - org.dishevelled.bio.tools.RenameBedReferences
  - org.dishevelled.bio.tools.RenameGff3References
  - org.dishevelled.bio.tools.RenameVcfReferences
- org.dishevelled.bio.tools.AbstractSplit (implements java.util.concurrent.Callable<V>)
  - org.dishevelled.bio.tools.SplitBed
  - org.dishevelled.bio.tools.SplitFasta
  - org.dishevelled.bio.tools.SplitFastq
  - org.dishevelled.bio.tools.SplitGaf
  - org.dishevelled.bio.tools.SplitGff3
  - org.dishevelled.bio.tools.SplitInterleavedFastq
  - org.dishevelled.bio.tools.SplitPaf
  - org.dishevelled.bio.tools.SplitSam
  - org.dishevelled.bio.tools.SplitVcf
- org.dishevelled.bio.tools.BinFastqQualityScores (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressBed (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressFasta (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressGaf (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressGfa1 (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressGfa2 (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressGff3 (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressPaf (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressRgfa (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressSam (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CompressVcf (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.CreateSequenceDictionary (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.DisinterleaveFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.DownsampleFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.DownsampleInterleavedFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.EnsemblVariantTableToVcf (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ExportSegments (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ExtractFasta (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ExtractFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ExtractFastqByLength (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastaToFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastaToText (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastqDescription (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastqSequenceLength (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastqToFasta (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FastqToText (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.FilterBed.RangeFilter (implements org.dishevelled.bio.tools.FilterBed.Filter)
- org.dishevelled.bio.tools.FilterBed.ScoreFilter (implements org.dishevelled.bio.tools.FilterBed.Filter)
- org.dishevelled.bio.tools.FilterBed.ScriptFilter (implements org.dishevelled.bio.tools.FilterBed.Filter)
- org.dishevelled.bio.tools.FilterFasta.LengthFilter (implements org.dishevelled.bio.tools.FilterFasta.Filter)
- org.dishevelled.bio.tools.FilterFasta.ScriptFilter (implements org.dishevelled.bio.tools.FilterFasta.Filter)
- org.dishevelled.bio.tools.FilterFastq.LengthFilter (implements org.dishevelled.bio.tools.FilterFastq.Filter)
- org.dishevelled.bio.tools.FilterFastq.ScriptFilter (implements org.dishevelled.bio.tools.FilterFastq.Filter)
- org.dishevelled.bio.tools.FilterGaf.MappingQualityFilter (implements org.dishevelled.bio.tools.FilterGaf.Filter)
- org.dishevelled.bio.tools.FilterGaf.QueryRangeFilter (implements org.dishevelled.bio.tools.FilterGaf.Filter)
- org.dishevelled.bio.tools.FilterGaf.ScriptFilter (implements org.dishevelled.bio.tools.FilterGaf.Filter)
- org.dishevelled.bio.tools.FilterGfa1.FragmentCountFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.KmerCountFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.LengthFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.MappingQualityFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.MismatchCountFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.ReadCountFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.ScriptFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa1.SegmentFilter (implements org.dishevelled.bio.tools.FilterGfa1.Filter)
- org.dishevelled.bio.tools.FilterGfa2.ScriptFilter (implements org.dishevelled.bio.tools.FilterGfa2.Filter)
- org.dishevelled.bio.tools.FilterGff3.RangeFilter (implements org.dishevelled.bio.tools.FilterGff3.Filter)
- org.dishevelled.bio.tools.FilterGff3.ScoreFilter (implements org.dishevelled.bio.tools.FilterGff3.Filter)
- org.dishevelled.bio.tools.FilterGff3.ScriptFilter (implements org.dishevelled.bio.tools.FilterGff3.Filter)
- org.dishevelled.bio.tools.FilterPaf.MappingQualityFilter (implements org.dishevelled.bio.tools.FilterPaf.Filter)
- org.dishevelled.bio.tools.FilterPaf.QueryRangeFilter (implements org.dishevelled.bio.tools.FilterPaf.Filter)
- org.dishevelled.bio.tools.FilterPaf.ScriptFilter (implements org.dishevelled.bio.tools.FilterPaf.Filter)
- org.dishevelled.bio.tools.FilterPaf.TargetRangeFilter (implements org.dishevelled.bio.tools.FilterPaf.Filter)
- org.dishevelled.bio.tools.FilterRgfa.FragmentCountFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.KmerCountFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.LengthFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.MappingQualityFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.MismatchCountFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.ReadCountFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.ScriptFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterRgfa.SegmentFilter (implements org.dishevelled.bio.tools.FilterRgfa.Filter)
- org.dishevelled.bio.tools.FilterSam.MapqFilter (implements org.dishevelled.bio.tools.FilterSam.Filter)
- org.dishevelled.bio.tools.FilterSam.RangeFilter (implements org.dishevelled.bio.tools.FilterSam.Filter)
- org.dishevelled.bio.tools.FilterSam.ScriptFilter (implements org.dishevelled.bio.tools.FilterSam.Filter)
- org.dishevelled.bio.tools.FilterVcf.FilterFilter (implements org.dishevelled.bio.tools.FilterVcf.Filter)
- org.dishevelled.bio.tools.FilterVcf.IdFilter (implements org.dishevelled.bio.tools.FilterVcf.Filter)
- org.dishevelled.bio.tools.FilterVcf.QualFilter (implements org.dishevelled.bio.tools.FilterVcf.Filter)
- org.dishevelled.bio.tools.FilterVcf.RangeFilter (implements org.dishevelled.bio.tools.FilterVcf.Filter)
- org.dishevelled.bio.tools.FilterVcf.ScriptFilter (implements org.dishevelled.bio.tools.FilterVcf.Filter)
- org.dishevelled.bio.tools.Gfa1ToGfa2 (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.IdentifyGfa1 (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.InterleaveFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.IntersectBed (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.LinksToCytoscapeEdges (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.LinksToPropertyGraph (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ListFilesystems (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.ReassemblePaths (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.RemapDbSnp (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.RemapPhaseSet (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.RenameReferences (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.SegmentsToCytoscapeNodes (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.SegmentsToPropertyGraph (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TextToFasta (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TextToFastq (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.Tools (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.Tools.Command
- org.dishevelled.bio.tools.TraversalsToCytoscapeEdges (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TraversalsToPropertyGraph (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TraversePaths (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TruncateFasta (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.TruncatePaths (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.VcfHeader (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.VcfPedigree (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.VcfSamples (implements java.util.concurrent.Callable<V>)
- org.dishevelled.bio.tools.WithReadGroup (implements java.util.concurrent.Callable<V>)
  - org.dishevelled.bio.tools.FastqToBam
  - org.dishevelled.bio.tools.InterleavedFastqToBam
- java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
  - java.io.FilterWriter
    - org.apache.commons.io.output.ProxyWriter
      - org.dishevelled.bio.tools.AbstractSplit.CountingWriter

Interface Hierarchy

org.dishevelled.bio.tools.FilterBed.Filter
org.dishevelled.bio.tools.FilterFasta.Filter
org.dishevelled.bio.tools.FilterFastq.Filter
org.dishevelled.bio.tools.FilterGaf.Filter
org.dishevelled.bio.tools.FilterGfa1.Filter
org.dishevelled.bio.tools.FilterGfa2.Filter
org.dishevelled.bio.tools.FilterGff3.Filter
org.dishevelled.bio.tools.FilterPaf.Filter
org.dishevelled.bio.tools.FilterRgfa.Filter
org.dishevelled.bio.tools.FilterSam.Filter
org.dishevelled.bio.tools.FilterVcf.Filter
org.dishevelled.bio.tools.IntersectBed.Strategy

Hierarchy For All Packages

Class Hierarchy

Interface Hierarchy