Package org.dishevelled.bio.tools

Command line tools.

See: Description

Interface Summary

Interface	Description
FilterBed.Filter	Filter.
FilterFasta.Filter	Filter.
FilterFastq.Filter	Filter.
FilterGaf.Filter	Filter.
FilterGfa1.Filter	Filter.
FilterGfa2.Filter	Filter.
FilterGff3.Filter	Filter.
FilterPaf.Filter	Filter.
FilterRgfa.Filter	Filter.
FilterSam.Filter	Filter.
FilterVcf.Filter	Filter.
IntersectBed.Strategy	Intersect BED strategy.

Class Summary

Class	Description
About	About.
AbstractFilter	Abstract filter callable.
AbstractRenameReferences	Abstract rename references callable.
AbstractSplit	Abstract split callable.
AbstractSplit.CountingWriter	Counting writer.
BinFastqQualityScores	Bin quality scores from files in FASTQ format.
CompressBed	Compress features in BED format to splittable bgzf or bzip2 compression codecs.
CompressFasta	Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFastq	Compress sequences in FASTQ format to splittable bgzf or bzip2 compression codecs.
CompressGaf	Compress alignments in GAF format to splittable bgzf or bzip2 compression codecs.
CompressGfa1	Compress assembly in GFA 1.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa2	Compress assembly in GFA 2.0 format to splittable bgzf or bzip2 compression codecs.
CompressGff3	Compress features in GFF3 format to splittable bgzf or bzip2 compression codecs.
CompressPaf	Compress alignments in PAF format to splittable bgzf or bzip2 compression codecs.
CompressRgfa	Compress assembly in rGFA format to splittable bgzf or bzip2 compression codecs.
CompressSam	Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.
CompressVcf	Compress variants or genotypes in VCF format to splittable bgzf or bzip2 compression codecs.
CreateSequenceDictionary	Create a SequenceDictionary from DNA sequences in FASTA format.
DisinterleaveFastq	Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
DownsampleFastq	Downsample DNA sequences from files in FASTQ format.
DownsampleInterleavedFastq	Downsample DNA sequences from a file in interleaved FASTQ format.
EnsemblVariantTableToVcf	Convert Ensembl variant table to VCF format.
ExportSegments	Export assembly segment sequences in GFA 1.0 format to FASTA format.
ExtractFasta	Extract matching DNA or protein sequences in FASTA format.
ExtractFastq	Extract matching DNA sequences in FASTQ format.
ExtractFastqByLength	Extract DNA sequences in FASTQ format with a range of lengths.
FastaToFastq	Convert DNA sequences in FASTA format to FASTQ format.
FastaToText	Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.
FastqDescription	Output description lines from DNA sequences in FASTQ format.
FastqSequenceLength	Output sequence lengths from DNA sequences in FASTQ format.
FastqToBam	Convert DNA sequences in FASTQ format to unaligned BAM format.
FastqToFasta	Convert DNA sequences in FASTQ format to FASTA format.
FastqToText	Convert DNA sequences in FASTQ format to tab-separated values (tsv) text format.
FilterBed	Filter features in BED format.
FilterBed.RangeFilter	Range filter.
FilterBed.ScoreFilter	Score filter.
FilterBed.ScriptFilter	Script filter.
FilterFasta	Filter DNA or protein sequences in FASTA format.
FilterFasta.LengthFilter	Length filter.
FilterFasta.ScriptFilter	Script filter.
FilterFastq	Filter sequences in FASTQ format.
FilterFastq.LengthFilter	Length filter.
FilterFastq.ScriptFilter	Script filter.
FilterGaf	Filter alignments in GAF format.
FilterGaf.MappingQualityFilter	Mapping quality filter.
FilterGaf.QueryRangeFilter	Query range filter.
FilterGaf.ScriptFilter	Script filter.
FilterGfa1	Filter assembly in GFA 1.0 format.
FilterGfa1.FragmentCountFilter	Fragment count filter.
FilterGfa1.KmerCountFilter	K-mer count filter.
FilterGfa1.LengthFilter	Length filter.
FilterGfa1.MappingQualityFilter	Mapping quality filter.
FilterGfa1.MismatchCountFilter	Mismatch count filter.
FilterGfa1.ReadCountFilter	Read count filter.
FilterGfa1.ScriptFilter	Script filter.
FilterGfa1.SegmentFilter	Segment filter.
FilterGfa2	Filter assembly in GFA 2.0 format.
FilterGfa2.ScriptFilter	Script filter.
FilterGff3	Filter features in GFF3 format.
FilterGff3.RangeFilter	Range filter.
FilterGff3.ScoreFilter	Score filter.
FilterGff3.ScriptFilter	Script filter.
FilterPaf	Filter alignments in PAF format.
FilterPaf.MappingQualityFilter	Mapping quality filter.
FilterPaf.QueryRangeFilter	Query range filter.
FilterPaf.ScriptFilter	Script filter.
FilterPaf.TargetRangeFilter	Target range filter.
FilterRgfa	Filter assembly in rGFA format.
FilterRgfa.FragmentCountFilter	Fragment count filter.
FilterRgfa.KmerCountFilter	K-mer count filter.
FilterRgfa.LengthFilter	Length filter.
FilterRgfa.MappingQualityFilter	Mapping quality filter.
FilterRgfa.MismatchCountFilter	Mismatch count filter.
FilterRgfa.ReadCountFilter	Read count filter.
FilterRgfa.ScriptFilter	Script filter.
FilterRgfa.SegmentFilter	Segment filter.
FilterSam	Filter alignments in SAM format.
FilterSam.MapqFilter	MAPQ filter.
FilterSam.RangeFilter	Range filter.
FilterSam.ScriptFilter	Script filter.
FilterVcf	Filter variants in VCF format.
FilterVcf.FilterFilter	Filter filter.
FilterVcf.IdFilter	Id filter.
FilterVcf.QualFilter	Quality score filter.
FilterVcf.RangeFilter	Range filter.
FilterVcf.ScriptFilter	Script filter.
Gfa1ToGfa2	Convert GFA 1.0 format to GFA 2.0 format.
IdentifyGfa1	Add identifier annotation to records in GFA 1.0 format.
InterleavedFastqToBam	Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
InterleaveFastq	Convert first and second DNA sequence files in FASTQ format to interleaved FASTQ format.
IntersectBed	Similar to bedtools2 intersect -v.
LinksToCytoscapeEdges	Convert links in GFA 1.0 format to edges.txt format for Cytoscape.
LinksToPropertyGraph	Convert links in GFA 1.0 format to property graph CSV format.
ListFilesystems	List installed filesystem providers.
ReassemblePaths	Reassemble paths in GFA 1.0 format, recreating segments and overlaps fields from traversal records.
RemapDbSnp	Remap DB Type=String flags in VCF format to DB Type=Flag and dbsnp Type=String fields.
RemapPhaseSet	Remap PS Type=String phase set ids in VCF format to PS Type=Integer.
RenameBedReferences	Rename references in BED files.
RenameGff3References	Rename references in GFF3 files.
RenameReferences	Deprecated by RenameGff3References in version 2.1, to be removed in 3.0
RenameVcfReferences	Rename references in VCF files.
SegmentsToCytoscapeNodes	Convert segments in GFA 1.0 format to nodes.txt format for Cytoscape.
SegmentsToPropertyGraph	Convert segments in GFA 1.0 format to property graph CSV format.
SplitBed	Split BED files.
SplitFasta	Split FASTA files.
SplitFastq	Split FASTQ files.
SplitGaf	Split GAF files.
SplitGff3	Split GFF3 files.
SplitInterleavedFastq	Split interleaved FASTQ files.
SplitPaf	Split PAF files.
SplitSam	Split SAM files.
SplitVcf	Split VCF files.
TextToFasta	Convert DNA or protein sequences in tab-separated values (tsv) text format to FASTA format.
TextToFastq	Convert DNA sequences in tab-separated values (tsv) text format to FASTQ format.
Tools	Command line tools.
Tools.Command	Command.
TraversalsToCytoscapeEdges	Convert traversals in GFA 1.0 format to edges.txt format for Cytoscape.
TraversalsToPropertyGraph	Convert traversals in GFA 1.0 format to property graph CSV format.
TraversePaths	Traverse paths in GFA 1.0 format, creating new traversal records.
TruncateFasta	Truncate DNA or protein sequences in FASTA format.
TruncatePaths	Truncate paths in GFA 1.0 format, removing segments and overlaps fields.
VcfHeader	Extract and validate header lines from VCF format.
VcfPedigree	Extract a pedigree from VCF format.
VcfSamples	Extract samples from VCF format.
WithReadGroup	Abstract callable with read group.

Package org.dishevelled.bio.tools Description

Command line tools.