org.dishevelled.bio.tools

Interfaces

• FilterBed.Filter
• FilterFasta.Filter
• FilterFastq.Filter
• FilterGaf.Filter
• FilterGfa1.Filter
• FilterGfa2.Filter
• FilterGff3.Filter
• FilterPaf.Filter
• FilterRgfa.Filter
• FilterSam.Filter
• FilterVcf.Filter
• IntersectBed.Strategy

Classes

• About
• AbstractFilter
• AbstractRenameReferences
• AbstractSplit
• AbstractSplit.CountingWriter
• BinFastqQualityScores
• CompressBed
• CompressFasta
• CompressFastq
• CompressGaf
• CompressGfa1
• CompressGfa2
• CompressGff3
• CompressPaf
• CompressRgfa
• CompressSam
• CompressVcf
• CreateSequenceDictionary
• DisinterleaveFastq
• DownsampleFastq
• DownsampleInterleavedFastq
• EnsemblVariantTableToVcf
• ExportSegments
• ExtractFasta
• ExtractFastq
• ExtractFastqByLength
• FastaToFastq
• FastaToText
• FastqDescription
• FastqSequenceLength
• FastqToBam
• FastqToFasta
• FastqToText
• FilterBed
• FilterBed.RangeFilter
• FilterBed.ScoreFilter
• FilterBed.ScriptFilter
• FilterFasta
• FilterFasta.LengthFilter
• FilterFasta.ScriptFilter
• FilterFastq
• FilterFastq.LengthFilter
• FilterFastq.ScriptFilter
• FilterGaf
• FilterGaf.MappingQualityFilter
• FilterGaf.QueryRangeFilter
• FilterGaf.ScriptFilter
• FilterGfa1
• FilterGfa1.FragmentCountFilter
• FilterGfa1.KmerCountFilter
• FilterGfa1.LengthFilter
• FilterGfa1.MappingQualityFilter
• FilterGfa1.MismatchCountFilter
• FilterGfa1.ReadCountFilter
• FilterGfa1.ScriptFilter
• FilterGfa1.SegmentFilter
• FilterGfa2
• FilterGfa2.ScriptFilter
• FilterGff3
• FilterGff3.RangeFilter
• FilterGff3.ScoreFilter
• FilterGff3.ScriptFilter
• FilterPaf
• FilterPaf.MappingQualityFilter
• FilterPaf.QueryRangeFilter
• FilterPaf.ScriptFilter
• FilterPaf.TargetRangeFilter
• FilterRgfa
• FilterRgfa.FragmentCountFilter
• FilterRgfa.KmerCountFilter
• FilterRgfa.LengthFilter
• FilterRgfa.MappingQualityFilter
• FilterRgfa.MismatchCountFilter
• FilterRgfa.ReadCountFilter
• FilterRgfa.ScriptFilter
• FilterRgfa.SegmentFilter
• FilterSam
• FilterSam.MapqFilter
• FilterSam.RangeFilter
• FilterSam.ScriptFilter
• FilterVcf
• FilterVcf.FilterFilter
• FilterVcf.IdFilter
• FilterVcf.QualFilter
• FilterVcf.RangeFilter
• FilterVcf.ScriptFilter
• Gfa1ToGfa2
• IdentifyGfa1
• InterleavedFastqToBam
• InterleaveFastq
• IntersectBed
• LinksToCytoscapeEdges
• LinksToPropertyGraph
• ListFilesystems
• ReassemblePaths
• RemapDbSnp
• RemapPhaseSet
• RenameBedReferences
• RenameGff3References
• RenameReferences
• RenameVcfReferences
• SegmentsToCytoscapeNodes
• SegmentsToPropertyGraph
• SplitBed
• SplitFasta
• SplitFastq
• SplitGaf
• SplitGff3
• SplitInterleavedFastq
• SplitPaf
• SplitSam
• SplitVcf
• TextToFasta
• TextToFastq
• Tools
• Tools.Command
• TraversalsToCytoscapeEdges
• TraversalsToPropertyGraph
• TraversePaths
• TruncateFasta
• TruncatePaths
• VcfHeader
• VcfPedigree
• VcfSamples
• WithReadGroup