Index (dsh-bio-tools 2.2 API)

A B C D E F G I K L M O Q R S T U V W

A

About - Class in org.dishevelled.bio.tools: About.
About() - Constructor for class org.dishevelled.bio.tools.About
about(PrintStream) - Static method in class org.dishevelled.bio.tools.About: Write about text to the specified print stream.
AbstractFilter - Class in org.dishevelled.bio.tools: Abstract filter callable.
AbstractFilter() - Constructor for class org.dishevelled.bio.tools.AbstractFilter
AbstractRenameReferences - Class in org.dishevelled.bio.tools: Abstract rename references callable.
AbstractRenameReferences(boolean, Path, File) - Constructor for class org.dishevelled.bio.tools.AbstractRenameReferences: Create a new rename references callable.
AbstractSplit - Class in org.dishevelled.bio.tools: Abstract split callable.
AbstractSplit(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.AbstractSplit: Abstract split callable.
AbstractSplit.CountingWriter - Class in org.dishevelled.bio.tools: Counting writer.
accept(BedRecord) - Method in interface org.dishevelled.bio.tools.FilterBed.Filter: Return true if the specified BED record should be accepted by this filter.
accept(BedRecord) - Method in class org.dishevelled.bio.tools.FilterBed.RangeFilter
accept(BedRecord) - Method in class org.dishevelled.bio.tools.FilterBed.ScoreFilter
accept(BedRecord) - Method in class org.dishevelled.bio.tools.FilterBed.ScriptFilter
accept(Sequence) - Method in interface org.dishevelled.bio.tools.FilterFasta.Filter: Return true if the specified FASTA sequence record should be accepted by this filter.
accept(Sequence) - Method in class org.dishevelled.bio.tools.FilterFasta.LengthFilter
accept(Sequence) - Method in class org.dishevelled.bio.tools.FilterFasta.ScriptFilter
accept(Fastq) - Method in interface org.dishevelled.bio.tools.FilterFastq.Filter: Return true if the specified FASTQ record should be accepted by this filter.
accept(Fastq) - Method in class org.dishevelled.bio.tools.FilterFastq.LengthFilter
accept(Fastq) - Method in class org.dishevelled.bio.tools.FilterFastq.ScriptFilter
accept(GafRecord) - Method in interface org.dishevelled.bio.tools.FilterGaf.Filter: Return true if the specified GAF record should be accepted by this filter.
accept(GafRecord) - Method in class org.dishevelled.bio.tools.FilterGaf.MappingQualityFilter
accept(GafRecord) - Method in class org.dishevelled.bio.tools.FilterGaf.QueryRangeFilter
accept(GafRecord) - Method in class org.dishevelled.bio.tools.FilterGaf.ScriptFilter
accept(Gfa1Record) - Method in interface org.dishevelled.bio.tools.FilterGfa1.Filter: Return true if the specified GFA 1.0 record should be accepted by this filter.
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.FragmentCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.KmerCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.LengthFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.MappingQualityFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.MismatchCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.ReadCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.ScriptFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterGfa1.SegmentFilter
accept(Gfa2Record) - Method in interface org.dishevelled.bio.tools.FilterGfa2.Filter: Return true if the specified GFA 2.0 record should be accepted by this filter.
accept(Gfa2Record) - Method in class org.dishevelled.bio.tools.FilterGfa2.ScriptFilter
accept(Gff3Record) - Method in interface org.dishevelled.bio.tools.FilterGff3.Filter: Return true if the specified GFF3 record should be accepted by this filter.
accept(Gff3Record) - Method in class org.dishevelled.bio.tools.FilterGff3.RangeFilter
accept(Gff3Record) - Method in class org.dishevelled.bio.tools.FilterGff3.ScoreFilter
accept(Gff3Record) - Method in class org.dishevelled.bio.tools.FilterGff3.ScriptFilter
accept(PafRecord) - Method in interface org.dishevelled.bio.tools.FilterPaf.Filter: Return true if the specified PAF record should be accepted by this filter.
accept(PafRecord) - Method in class org.dishevelled.bio.tools.FilterPaf.MappingQualityFilter
accept(PafRecord) - Method in class org.dishevelled.bio.tools.FilterPaf.QueryRangeFilter
accept(PafRecord) - Method in class org.dishevelled.bio.tools.FilterPaf.ScriptFilter
accept(PafRecord) - Method in class org.dishevelled.bio.tools.FilterPaf.TargetRangeFilter
accept(Gfa1Record) - Method in interface org.dishevelled.bio.tools.FilterRgfa.Filter: Return true if the specified rGFA record should be accepted by this filter.
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.FragmentCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.KmerCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.LengthFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.MappingQualityFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.MismatchCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.ReadCountFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.ScriptFilter
accept(Gfa1Record) - Method in class org.dishevelled.bio.tools.FilterRgfa.SegmentFilter
accept(SamRecord) - Method in interface org.dishevelled.bio.tools.FilterSam.Filter: Return true if the specified SAM record should be accepted by this filter.
accept(SamRecord) - Method in class org.dishevelled.bio.tools.FilterSam.MapqFilter
accept(SamRecord) - Method in class org.dishevelled.bio.tools.FilterSam.RangeFilter
accept(SamRecord) - Method in class org.dishevelled.bio.tools.FilterSam.ScriptFilter
accept(VcfRecord) - Method in interface org.dishevelled.bio.tools.FilterVcf.Filter: Return true if the specified VCF record should be accepted by this filter.
accept(VcfRecord) - Method in class org.dishevelled.bio.tools.FilterVcf.FilterFilter
accept(VcfRecord) - Method in class org.dishevelled.bio.tools.FilterVcf.IdFilter
accept(VcfRecord) - Method in class org.dishevelled.bio.tools.FilterVcf.QualFilter
accept(VcfRecord) - Method in class org.dishevelled.bio.tools.FilterVcf.RangeFilter
accept(VcfRecord) - Method in class org.dishevelled.bio.tools.FilterVcf.ScriptFilter
addChr(String) - Static method in class org.dishevelled.bio.tools.AbstractRenameReferences: Add "chr" to the specified reference name.
addChr(String) - Static method in class org.dishevelled.bio.tools.RenameReferences: Deprecated.
artifactId() - Method in class org.dishevelled.bio.tools.About: Return the artifact id.
asPrintWriter() - Method in class org.dishevelled.bio.tools.AbstractSplit.CountingWriter: Return this counting writer wrapped in a PrintWriter.

B

beforeWrite(int) - Method in class org.dishevelled.bio.tools.AbstractSplit.CountingWriter
bin(String) - Static method in class org.dishevelled.bio.tools.BinFastqQualityScores: Bin the specified quality scores per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."
BinFastqQualityScores - Class in org.dishevelled.bio.tools: Bin quality scores from files in FASTQ format.
BinFastqQualityScores(Path, File) - Constructor for class org.dishevelled.bio.tools.BinFastqQualityScores: Bin quality scores from files in FASTQ format.
binQualityScore(int) - Static method in class org.dishevelled.bio.tools.BinFastqQualityScores: Bin the specified quality score per Illumina technical note, "Reducing Whole-Genome Data Storage Footprint."
buildTimestamp() - Method in class org.dishevelled.bio.tools.About: Return the build timestamp.
bytes - Variable in class org.dishevelled.bio.tools.AbstractSplit: Split the input path at the next record after each n bytes, if any.

C

call() - Method in class org.dishevelled.bio.tools.BinFastqQualityScores
call() - Method in class org.dishevelled.bio.tools.CompressBed
call() - Method in class org.dishevelled.bio.tools.CompressFasta
call() - Method in class org.dishevelled.bio.tools.CompressFastq
call() - Method in class org.dishevelled.bio.tools.CompressGaf
call() - Method in class org.dishevelled.bio.tools.CompressGfa1
call() - Method in class org.dishevelled.bio.tools.CompressGfa2
call() - Method in class org.dishevelled.bio.tools.CompressGff3
call() - Method in class org.dishevelled.bio.tools.CompressPaf
call() - Method in class org.dishevelled.bio.tools.CompressRgfa
call() - Method in class org.dishevelled.bio.tools.CompressSam
call() - Method in class org.dishevelled.bio.tools.CompressVcf
call() - Method in class org.dishevelled.bio.tools.CreateSequenceDictionary
call() - Method in class org.dishevelled.bio.tools.DisinterleaveFastq
call() - Method in class org.dishevelled.bio.tools.DownsampleFastq
call() - Method in class org.dishevelled.bio.tools.DownsampleInterleavedFastq
call() - Method in class org.dishevelled.bio.tools.EnsemblVariantTableToVcf
call() - Method in class org.dishevelled.bio.tools.ExportSegments
call() - Method in class org.dishevelled.bio.tools.ExtractFasta
call() - Method in class org.dishevelled.bio.tools.ExtractFastq
call() - Method in class org.dishevelled.bio.tools.ExtractFastqByLength
call() - Method in class org.dishevelled.bio.tools.FastaToFastq
call() - Method in class org.dishevelled.bio.tools.FastaToText
call() - Method in class org.dishevelled.bio.tools.FastqDescription
call() - Method in class org.dishevelled.bio.tools.FastqSequenceLength
call() - Method in class org.dishevelled.bio.tools.FastqToBam
call() - Method in class org.dishevelled.bio.tools.FastqToFasta
call() - Method in class org.dishevelled.bio.tools.FastqToText
call() - Method in class org.dishevelled.bio.tools.FilterBed
call() - Method in class org.dishevelled.bio.tools.FilterFasta
call() - Method in class org.dishevelled.bio.tools.FilterFastq
call() - Method in class org.dishevelled.bio.tools.FilterGaf
call() - Method in class org.dishevelled.bio.tools.FilterGfa1
call() - Method in class org.dishevelled.bio.tools.FilterGfa2
call() - Method in class org.dishevelled.bio.tools.FilterGff3
call() - Method in class org.dishevelled.bio.tools.FilterPaf
call() - Method in class org.dishevelled.bio.tools.FilterRgfa
call() - Method in class org.dishevelled.bio.tools.FilterSam
call() - Method in class org.dishevelled.bio.tools.FilterVcf
call() - Method in class org.dishevelled.bio.tools.Gfa1ToGfa2
call() - Method in class org.dishevelled.bio.tools.IdentifyGfa1
call() - Method in class org.dishevelled.bio.tools.InterleavedFastqToBam
call() - Method in class org.dishevelled.bio.tools.InterleaveFastq
call() - Method in class org.dishevelled.bio.tools.IntersectBed
call() - Method in class org.dishevelled.bio.tools.LinksToCytoscapeEdges
call() - Method in class org.dishevelled.bio.tools.LinksToPropertyGraph
call() - Method in class org.dishevelled.bio.tools.ListFilesystems
call() - Method in class org.dishevelled.bio.tools.ReassemblePaths
call() - Method in class org.dishevelled.bio.tools.RemapDbSnp
call() - Method in class org.dishevelled.bio.tools.RemapPhaseSet
call() - Method in class org.dishevelled.bio.tools.RenameBedReferences
call() - Method in class org.dishevelled.bio.tools.RenameGff3References
call() - Method in class org.dishevelled.bio.tools.RenameReferences: Deprecated.
call() - Method in class org.dishevelled.bio.tools.RenameVcfReferences
call() - Method in class org.dishevelled.bio.tools.SegmentsToCytoscapeNodes
call() - Method in class org.dishevelled.bio.tools.SegmentsToPropertyGraph
call() - Method in class org.dishevelled.bio.tools.SplitBed
call() - Method in class org.dishevelled.bio.tools.SplitFasta
call() - Method in class org.dishevelled.bio.tools.SplitFastq
call() - Method in class org.dishevelled.bio.tools.SplitGaf
call() - Method in class org.dishevelled.bio.tools.SplitGff3
call() - Method in class org.dishevelled.bio.tools.SplitInterleavedFastq
call() - Method in class org.dishevelled.bio.tools.SplitPaf
call() - Method in class org.dishevelled.bio.tools.SplitSam
call() - Method in class org.dishevelled.bio.tools.SplitVcf
call() - Method in class org.dishevelled.bio.tools.TextToFasta
call() - Method in class org.dishevelled.bio.tools.TextToFastq
call() - Method in class org.dishevelled.bio.tools.Tools
call() - Method in class org.dishevelled.bio.tools.TraversalsToCytoscapeEdges
call() - Method in class org.dishevelled.bio.tools.TraversalsToPropertyGraph
call() - Method in class org.dishevelled.bio.tools.TraversePaths
call() - Method in class org.dishevelled.bio.tools.TruncateFasta
call() - Method in class org.dishevelled.bio.tools.TruncatePaths
call() - Method in class org.dishevelled.bio.tools.VcfHeader
call() - Method in class org.dishevelled.bio.tools.VcfPedigree
call() - Method in class org.dishevelled.bio.tools.VcfSamples
closeWriters() - Method in class org.dishevelled.bio.tools.AbstractSplit: Attempt to close writers created by createCountingWriter.
Command(String, String, Class<?>) - Constructor for class org.dishevelled.bio.tools.Tools.Command: Create a new command.
COMMANDS - Static variable in class org.dishevelled.bio.tools.Tools: Map of commands keyed by command name.
commit() - Method in class org.dishevelled.bio.tools.About: Return the last commit.
CompressBed - Class in org.dishevelled.bio.tools: Compress features in BED format to splittable bgzf or bzip2 compression codecs.
CompressBed(File, File) - Constructor for class org.dishevelled.bio.tools.CompressBed: Compress features in BED format to splittable bgzf or bzip2 compression codecs.
CompressBed(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressBed: Compress features in BED format to splittable bgzf or bzip2 compression codecs.
CompressFasta - Class in org.dishevelled.bio.tools: Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(File, File, int) - Constructor for class org.dishevelled.bio.tools.CompressFasta: Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(Path, File, int) - Constructor for class org.dishevelled.bio.tools.CompressFasta: Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(File, File, String, int) - Constructor for class org.dishevelled.bio.tools.CompressFasta: Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(Path, File, String, int) - Constructor for class org.dishevelled.bio.tools.CompressFasta: Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFastq - Class in org.dishevelled.bio.tools: Compress sequences in FASTQ format to splittable bgzf or bzip2 compression codecs.
CompressFastq(File, File) - Constructor for class org.dishevelled.bio.tools.CompressFastq: Compress sequences in FASTQ format to splittable bgzf or bzip2 compression codecs.
CompressFastq(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressFastq: Compress sequences in FASTQ format to splittable bgzf or bzip2 compression codecs.
CompressGaf - Class in org.dishevelled.bio.tools: Compress alignments in GAF format to splittable bgzf or bzip2 compression codecs.
CompressGaf(File, File) - Constructor for class org.dishevelled.bio.tools.CompressGaf: Compress alignments in GAF format to splittable bgzf or bzip2 compression codecs.
CompressGaf(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressGaf: Compress alignments in GAF format to splittable bgzf or bzip2 compression codecs.
CompressGfa1 - Class in org.dishevelled.bio.tools: Compress assembly in GFA 1.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa1(File, File) - Constructor for class org.dishevelled.bio.tools.CompressGfa1: Compress assembly in GFA 1.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa1(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressGfa1: Compress assembly in GFA 1.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa2 - Class in org.dishevelled.bio.tools: Compress assembly in GFA 2.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa2(File, File) - Constructor for class org.dishevelled.bio.tools.CompressGfa2: Compress assembly in GFA 2.0 format to splittable bgzf or bzip2 compression codecs.
CompressGfa2(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressGfa2: Compress assembly in GFA 2.0 format to splittable bgzf or bzip2 compression codecs.
CompressGff3 - Class in org.dishevelled.bio.tools: Compress features in GFF3 format to splittable bgzf or bzip2 compression codecs.
CompressGff3(File, File) - Constructor for class org.dishevelled.bio.tools.CompressGff3: Compress features in GFF3 format to splittable bgzf or bzip2 compression codecs.
CompressGff3(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressGff3: Compress features in GFF3 format to splittable bgzf or bzip2 compression codecs.
CompressPaf - Class in org.dishevelled.bio.tools: Compress alignments in PAF format to splittable bgzf or bzip2 compression codecs.
CompressPaf(File, File) - Constructor for class org.dishevelled.bio.tools.CompressPaf: Compress alignments in PAF format to splittable bgzf or bzip2 compression codecs.
CompressPaf(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressPaf: Compress alignments in PAF format to splittable bgzf or bzip2 compression codecs.
CompressRgfa - Class in org.dishevelled.bio.tools: Compress assembly in rGFA format to splittable bgzf or bzip2 compression codecs.
CompressRgfa(File, File) - Constructor for class org.dishevelled.bio.tools.CompressRgfa: Compress assembly in rGFA format to splittable bgzf or bzip2 compression codecs.
CompressRgfa(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressRgfa: Compress assembly in rGFA format to splittable bgzf or bzip2 compression codecs.
CompressSam - Class in org.dishevelled.bio.tools: Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.
CompressSam(File, File) - Constructor for class org.dishevelled.bio.tools.CompressSam: Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.
CompressSam(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressSam: Compress alignments in SAM format to splittable bgzf or bzip2 compression codecs.
CompressVcf - Class in org.dishevelled.bio.tools: Compress variants or genotypes in VCF format to splittable bgzf or bzip2 compression codecs.
CompressVcf(File, File) - Constructor for class org.dishevelled.bio.tools.CompressVcf: Compress variants or genotypes in VCF format to splittable bgzf or bzip2 compression codecs.
CompressVcf(Path, File) - Constructor for class org.dishevelled.bio.tools.CompressVcf: Compress variants or genotypes in VCF format to splittable bgzf or bzip2 compression codecs.
convert(Fastq) - Method in class org.dishevelled.bio.tools.FastqToBam
convertLeft(Fastq) - Method in class org.dishevelled.bio.tools.InterleavedFastqToBam
convertRight(Fastq) - Method in class org.dishevelled.bio.tools.InterleavedFastqToBam
copyright() - Method in class org.dishevelled.bio.tools.About: Return the copyright.
createCountingWriter(int) - Method in class org.dishevelled.bio.tools.AbstractSplit: Create and return a new CountingWriter for a file name consisting of prefix + n + suffix.
createReadGroupBarcodesArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group barcodes commandline argument.
createReadGroupIdArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group id commandline argument.
createReadGroupInsertSizeArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group insert size commandline argument.
createReadGroupLibraryArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group library commandline argument.
createReadGroupPlatformUnitArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group platform unit commandline argument.
createReadGroupSampleArgument() - Static method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group sample commandline argument.
createScriptEngine() - Static method in class org.dishevelled.bio.tools.AbstractFilter: Create and return a new script engine.
CreateSequenceDictionary - Class in org.dishevelled.bio.tools: Create a SequenceDictionary from DNA sequences in FASTA format.
CreateSequenceDictionary(File, File) - Constructor for class org.dishevelled.bio.tools.CreateSequenceDictionary: Create a SequenceDictionary from DNA sequences in FASTA format.
CreateSequenceDictionary(Path, File) - Constructor for class org.dishevelled.bio.tools.CreateSequenceDictionary: Create a SequenceDictionary from DNA sequences in FASTA format.
CreateSequenceDictionary(URL, File, File) - Constructor for class org.dishevelled.bio.tools.CreateSequenceDictionary: Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.
CreateSequenceDictionary(URL, Path, File) - Constructor for class org.dishevelled.bio.tools.CreateSequenceDictionary: Create a SequenceDictionary from DNA sequences in FASTA format with the specified URL.

D

DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.CompressFasta
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.ExtractFasta
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.FastaToText
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.FilterFasta
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.SplitFasta
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.TextToFasta
DEFAULT_ALPHABET - Static variable in class org.dishevelled.bio.tools.TruncateFasta
DEFAULT_LENGTH - Static variable in class org.dishevelled.bio.tools.TruncateFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.CompressFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.ExportSegments
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.ExtractFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.FilterFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.SplitFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.TextToFasta
DEFAULT_LINE_WIDTH - Static variable in class org.dishevelled.bio.tools.TruncateFasta
DEFAULT_QUALITY - Static variable in class org.dishevelled.bio.tools.FastaToFastq
describeSegment(Segment) - Static method in class org.dishevelled.bio.tools.ExportSegments
describeSequence(Sequence) - Static method in class org.dishevelled.bio.tools.CompressFasta
describeSequence(Sequence) - Static method in class org.dishevelled.bio.tools.ExtractFasta
describeSequence(Sequence) - Static method in class org.dishevelled.bio.tools.FilterFasta
describeSequence(Sequence) - Static method in class org.dishevelled.bio.tools.SplitFasta
describeSequence(Sequence) - Static method in class org.dishevelled.bio.tools.TruncateFasta
DESCRIPTION_LINE - Static variable in class org.dishevelled.bio.tools.CompressFasta
DESCRIPTION_LINE - Static variable in class org.dishevelled.bio.tools.ExtractFasta
DESCRIPTION_LINE - Static variable in class org.dishevelled.bio.tools.FilterFasta
DESCRIPTION_LINE - Static variable in class org.dishevelled.bio.tools.SplitFasta
DESCRIPTION_LINE - Static variable in class org.dishevelled.bio.tools.TruncateFasta
DisinterleaveFastq - Class in org.dishevelled.bio.tools: Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
DisinterleaveFastq(File, File, File, File) - Constructor for class org.dishevelled.bio.tools.DisinterleaveFastq: Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
DisinterleaveFastq(Path, Path, File, File) - Constructor for class org.dishevelled.bio.tools.DisinterleaveFastq: Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
DownsampleFastq - Class in org.dishevelled.bio.tools: Downsample DNA sequences from files in FASTQ format.
DownsampleFastq(File, File, BinomialDistribution) - Constructor for class org.dishevelled.bio.tools.DownsampleFastq: Downsample DNA sequences from files in FASTQ format.
DownsampleFastq(Path, File, BinomialDistribution) - Constructor for class org.dishevelled.bio.tools.DownsampleFastq: Downsample DNA sequences from files in FASTQ format.
DownsampleInterleavedFastq - Class in org.dishevelled.bio.tools: Downsample DNA sequences from a file in interleaved FASTQ format.
DownsampleInterleavedFastq(File, File, BinomialDistribution) - Constructor for class org.dishevelled.bio.tools.DownsampleInterleavedFastq: Downsample DNA sequences from a file in interleaved FASTQ format.
DownsampleInterleavedFastq(Path, File, BinomialDistribution) - Constructor for class org.dishevelled.bio.tools.DownsampleInterleavedFastq: Downsample DNA sequences from a file in interleaved FASTQ format.
dropFirst(String[]) - Static method in class org.dishevelled.bio.tools.Tools: Drop the first element from the specified array.

E

EnsemblVariantTableToVcf - Class in org.dishevelled.bio.tools: Convert Ensembl variant table to VCF format.
EnsemblVariantTableToVcf(File, File) - Constructor for class org.dishevelled.bio.tools.EnsemblVariantTableToVcf: Convert Ensembl variant table to VCF format
EnsemblVariantTableToVcf(Path, File) - Constructor for class org.dishevelled.bio.tools.EnsemblVariantTableToVcf: Convert Ensembl variant table to VCF format
ExportSegments - Class in org.dishevelled.bio.tools: Export assembly segment sequences in GFA 1.0 format to FASTA format.
ExportSegments(File, File, int) - Constructor for class org.dishevelled.bio.tools.ExportSegments: Export assembly segment sequences in GFA 1.0 format to FASTA format.
ExportSegments(Path, File, int) - Constructor for class org.dishevelled.bio.tools.ExportSegments: Export assembly segment sequences in GFA 1.0 format to FASTA format.
ExtractFasta - Class in org.dishevelled.bio.tools: Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(File, File, String, String, int) - Constructor for class org.dishevelled.bio.tools.ExtractFasta: Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(Path, File, String, String, int) - Constructor for class org.dishevelled.bio.tools.ExtractFasta: Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(File, File, String, String, String, int) - Constructor for class org.dishevelled.bio.tools.ExtractFasta: Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(Path, File, String, String, String, int) - Constructor for class org.dishevelled.bio.tools.ExtractFasta: Extract matching DNA or protein sequences in FASTA format.
ExtractFastq - Class in org.dishevelled.bio.tools: Extract matching DNA sequences in FASTQ format.
ExtractFastq(File, File, String, String) - Constructor for class org.dishevelled.bio.tools.ExtractFastq: Extract matching DNA sequences in FASTQ format.
ExtractFastq(Path, File, String, String) - Constructor for class org.dishevelled.bio.tools.ExtractFastq: Extract matching DNA sequences in FASTQ format.
ExtractFastqByLength - Class in org.dishevelled.bio.tools: Extract DNA sequences in FASTQ format with a range of lengths.
ExtractFastqByLength(File, File, int, int) - Constructor for class org.dishevelled.bio.tools.ExtractFastqByLength: Extract DNA sequences in FASTQ format with a range of lengths.
ExtractFastqByLength(Path, File, int, int) - Constructor for class org.dishevelled.bio.tools.ExtractFastqByLength: Extract DNA sequences in FASTQ format with a range of lengths.

F

FastaToFastq - Class in org.dishevelled.bio.tools: Convert DNA sequences in FASTA format to FASTQ format.
FastaToFastq(File, File, int) - Constructor for class org.dishevelled.bio.tools.FastaToFastq: Convert DNA sequences in FASTA format to FASTQ format.
FastaToFastq(Path, File, int) - Constructor for class org.dishevelled.bio.tools.FastaToFastq: Convert DNA sequences in FASTA format to FASTQ format.
FastaToText - Class in org.dishevelled.bio.tools: Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.
FastaToText(Path, File, String) - Constructor for class org.dishevelled.bio.tools.FastaToText: Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.
FastqDescription - Class in org.dishevelled.bio.tools: Output description lines from DNA sequences in FASTQ format.
FastqDescription(File, File) - Constructor for class org.dishevelled.bio.tools.FastqDescription: Output description lines from DNA sequences in FASTQ format.
FastqDescription(Path, File) - Constructor for class org.dishevelled.bio.tools.FastqDescription: Output description lines from DNA sequences in FASTQ format.
FastqSequenceLength - Class in org.dishevelled.bio.tools: Output sequence lengths from DNA sequences in FASTQ format.
FastqSequenceLength(File, File) - Constructor for class org.dishevelled.bio.tools.FastqSequenceLength: Output sequence lengths from DNA sequences in FASTQ format.
FastqSequenceLength(Path, File) - Constructor for class org.dishevelled.bio.tools.FastqSequenceLength: Output sequence lengths from DNA sequences in FASTQ format.
FastqToBam - Class in org.dishevelled.bio.tools: Convert DNA sequences in FASTQ format to unaligned BAM format.
FastqToBam(File, File, String, String, String, String, Integer, List<String>) - Constructor for class org.dishevelled.bio.tools.FastqToBam: Convert DNA sequences in FASTQ format to unaligned BAM format.
FastqToBam(Path, File, String, String, String, String, Integer, List<String>) - Constructor for class org.dishevelled.bio.tools.FastqToBam: Convert DNA sequences in FASTQ format to unaligned BAM format.
FastqToFasta - Class in org.dishevelled.bio.tools: Convert DNA sequences in FASTQ format to FASTA format.
FastqToFasta(File, File) - Constructor for class org.dishevelled.bio.tools.FastqToFasta: Convert DNA sequences in FASTQ format to FASTA format.
FastqToFasta(Path, File) - Constructor for class org.dishevelled.bio.tools.FastqToFasta: Convert DNA sequences in FASTQ format to FASTA format.
FastqToText - Class in org.dishevelled.bio.tools: Convert DNA sequences in FASTQ format to tab-separated values (tsv) text format.
FastqToText(File, File) - Constructor for class org.dishevelled.bio.tools.FastqToText: Convert DNA sequences in FASTQ format to tab-separated values (tsv) text format.
FastqToText(Path, File) - Constructor for class org.dishevelled.bio.tools.FastqToText: Convert DNA sequences in FASTQ format to tab-separated values (tsv) text format.
FilterBed - Class in org.dishevelled.bio.tools: Filter features in BED format.
FilterBed(List<FilterBed.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterBed: Filter features in BED format.
FilterBed(List<FilterBed.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterBed: Filter features in BED format.
FilterBed.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterBed.RangeFilter - Class in org.dishevelled.bio.tools: Range filter.
FilterBed.ScoreFilter - Class in org.dishevelled.bio.tools: Score filter.
FilterBed.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterFasta - Class in org.dishevelled.bio.tools: Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter>, File, File, int) - Constructor for class org.dishevelled.bio.tools.FilterFasta: Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter>, Path, File, int) - Constructor for class org.dishevelled.bio.tools.FilterFasta: Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter>, File, File, String, int) - Constructor for class org.dishevelled.bio.tools.FilterFasta: Filter DNA or protein sequences in FASTA format.
FilterFasta(List<FilterFasta.Filter>, Path, File, String, int) - Constructor for class org.dishevelled.bio.tools.FilterFasta: Filter DNA or protein sequences in FASTA format.
FilterFasta.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterFasta.LengthFilter - Class in org.dishevelled.bio.tools: Length filter.
FilterFasta.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterFastq - Class in org.dishevelled.bio.tools: Filter sequences in FASTQ format.
FilterFastq(List<FilterFastq.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterFastq: Filter sequences in FASTQ format.
FilterFastq(List<FilterFastq.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterFastq: Filter sequences in FASTQ format.
FilterFastq.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterFastq.LengthFilter - Class in org.dishevelled.bio.tools: Length filter.
FilterFastq.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterFilter() - Constructor for class org.dishevelled.bio.tools.FilterVcf.FilterFilter
FilterGaf - Class in org.dishevelled.bio.tools: Filter alignments in GAF format.
FilterGaf(List<FilterGaf.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterGaf: Filter alignments in GAF format.
FilterGaf(List<FilterGaf.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterGaf: Filter alignments in GAF format.
FilterGaf.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterGaf.MappingQualityFilter - Class in org.dishevelled.bio.tools: Mapping quality filter.
FilterGaf.QueryRangeFilter - Class in org.dishevelled.bio.tools: Query range filter.
FilterGaf.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterGfa1 - Class in org.dishevelled.bio.tools: Filter assembly in GFA 1.0 format.
FilterGfa1(List<FilterGfa1.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterGfa1: Filter assembly in GFA 1.0 format.
FilterGfa1(List<FilterGfa1.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterGfa1: Filter assembly in GFA 1.0 format.
FilterGfa1.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterGfa1.FragmentCountFilter - Class in org.dishevelled.bio.tools: Fragment count filter.
FilterGfa1.KmerCountFilter - Class in org.dishevelled.bio.tools: K-mer count filter.
FilterGfa1.LengthFilter - Class in org.dishevelled.bio.tools: Length filter.
FilterGfa1.MappingQualityFilter - Class in org.dishevelled.bio.tools: Mapping quality filter.
FilterGfa1.MismatchCountFilter - Class in org.dishevelled.bio.tools: Mismatch count filter.
FilterGfa1.ReadCountFilter - Class in org.dishevelled.bio.tools: Read count filter.
FilterGfa1.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterGfa1.SegmentFilter - Class in org.dishevelled.bio.tools: Segment filter.
FilterGfa2 - Class in org.dishevelled.bio.tools: Filter assembly in GFA 2.0 format.
FilterGfa2(List<FilterGfa2.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterGfa2: Filter assembly in GFA2 format.
FilterGfa2(List<FilterGfa2.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterGfa2: Filter assembly in GFA2 format.
FilterGfa2.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterGfa2.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterGff3 - Class in org.dishevelled.bio.tools: Filter features in GFF3 format.
FilterGff3(List<FilterGff3.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterGff3: Filter features in GFF3 format.
FilterGff3(List<FilterGff3.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterGff3: Filter features in GFF3 format.
FilterGff3.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterGff3.RangeFilter - Class in org.dishevelled.bio.tools: Range filter.
FilterGff3.ScoreFilter - Class in org.dishevelled.bio.tools: Score filter.
FilterGff3.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterPaf - Class in org.dishevelled.bio.tools: Filter alignments in PAF format.
FilterPaf(List<FilterPaf.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterPaf: Filter alignments in PAF format.
FilterPaf(List<FilterPaf.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterPaf: Filter alignments in PAF format.
FilterPaf.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterPaf.MappingQualityFilter - Class in org.dishevelled.bio.tools: Mapping quality filter.
FilterPaf.QueryRangeFilter - Class in org.dishevelled.bio.tools: Query range filter.
FilterPaf.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterPaf.TargetRangeFilter - Class in org.dishevelled.bio.tools: Target range filter.
FilterRgfa - Class in org.dishevelled.bio.tools: Filter assembly in rGFA format.
FilterRgfa(List<FilterRgfa.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterRgfa: Filter assembly in rGFA format.
FilterRgfa(List<FilterRgfa.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterRgfa: Filter assembly in rGFA format.
FilterRgfa.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterRgfa.FragmentCountFilter - Class in org.dishevelled.bio.tools: Fragment count filter.
FilterRgfa.KmerCountFilter - Class in org.dishevelled.bio.tools: K-mer count filter.
FilterRgfa.LengthFilter - Class in org.dishevelled.bio.tools: Length filter.
FilterRgfa.MappingQualityFilter - Class in org.dishevelled.bio.tools: Mapping quality filter.
FilterRgfa.MismatchCountFilter - Class in org.dishevelled.bio.tools: Mismatch count filter.
FilterRgfa.ReadCountFilter - Class in org.dishevelled.bio.tools: Read count filter.
FilterRgfa.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterRgfa.SegmentFilter - Class in org.dishevelled.bio.tools: Segment filter.
FilterSam - Class in org.dishevelled.bio.tools: Filter alignments in SAM format.
FilterSam(List<FilterSam.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterSam: Filter alignments in SAM format.
FilterSam(List<FilterSam.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterSam: Filter alignments in SAM format.
FilterSam.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterSam.MapqFilter - Class in org.dishevelled.bio.tools: MAPQ filter.
FilterSam.RangeFilter - Class in org.dishevelled.bio.tools: Range filter.
FilterSam.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
FilterVcf - Class in org.dishevelled.bio.tools: Filter variants in VCF format.
FilterVcf(List<FilterVcf.Filter>, File, File) - Constructor for class org.dishevelled.bio.tools.FilterVcf: Filter variants in VCF format.
FilterVcf(List<FilterVcf.Filter>, Path, File) - Constructor for class org.dishevelled.bio.tools.FilterVcf: Filter variants in VCF format.
FilterVcf.Filter - Interface in org.dishevelled.bio.tools: Filter.
FilterVcf.FilterFilter - Class in org.dishevelled.bio.tools: Filter filter.
FilterVcf.IdFilter - Class in org.dishevelled.bio.tools: Id filter.
FilterVcf.QualFilter - Class in org.dishevelled.bio.tools: Quality score filter.
FilterVcf.RangeFilter - Class in org.dishevelled.bio.tools: Range filter.
FilterVcf.ScriptFilter - Class in org.dishevelled.bio.tools: Script filter.
first(String[]) - Static method in class org.dishevelled.bio.tools.Tools: Return an array containing the first element of the specified array.
FragmentCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.FragmentCountFilter: Create a new fragment count filter with the specified fragment count.
FragmentCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.FragmentCountFilter: Create a new fragment count filter with the specified fragment count.

G

getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitBed
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitFasta
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitFastq
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitGaf
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitGff3
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitInterleavedFastq
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitPaf
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitSam
getBaseName(Path) - Static method in class org.dishevelled.bio.tools.SplitVcf
getCommandClass() - Method in class org.dishevelled.bio.tools.Tools.Command: Return the class for this command.
getCount() - Method in class org.dishevelled.bio.tools.AbstractSplit.CountingWriter: Return the count of chars written to the writer proxied by this counting writer.
getDescription() - Method in class org.dishevelled.bio.tools.Tools.Command: Return the description for this command.
getFileExtension(Path) - Static method in class org.dishevelled.bio.tools.AbstractSplit
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitBed
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitFasta
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitFastq
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitGaf
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitGff3
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitInterleavedFastq
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitPaf
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitSam
getFileExtensions(Path) - Static method in class org.dishevelled.bio.tools.SplitVcf
getName() - Method in class org.dishevelled.bio.tools.Tools.Command: Return the name for this command.
getNameWithoutExtension(Path) - Static method in class org.dishevelled.bio.tools.AbstractSplit
getReadGroupBarcodes() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the list of read group barcodes, if any.
getReadGroupId() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the read group id, if any.
getReadGroupInsertSize() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the read group insert size, if any.
getReadGroupLibrary() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the read group library, if any.
getReadGroupPlatformUnit() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the read group platform unit, if any.
getReadGroupSample() - Method in class org.dishevelled.bio.tools.WithReadGroup: Return the read group sample, if any.
Gfa1ToGfa2 - Class in org.dishevelled.bio.tools: Convert GFA 1.0 format to GFA 2.0 format.
Gfa1ToGfa2(File, File) - Constructor for class org.dishevelled.bio.tools.Gfa1ToGfa2: Convert GFA 1.0 format to GFA 2.0 format.
Gfa1ToGfa2(Path, File) - Constructor for class org.dishevelled.bio.tools.Gfa1ToGfa2: Convert GFA 1.0 format to GFA 2.0 format.

I

IdentifyGfa1 - Class in org.dishevelled.bio.tools: Add identifier annotation to records in GFA 1.0 format.
IdentifyGfa1(File, File) - Constructor for class org.dishevelled.bio.tools.IdentifyGfa1: Add identifier annotation to records in GFA 1.0 format.
IdentifyGfa1(Path, File) - Constructor for class org.dishevelled.bio.tools.IdentifyGfa1: Add identifier annotation to records in GFA 1.0 format.
IdFilter(List<String>) - Constructor for class org.dishevelled.bio.tools.FilterVcf.IdFilter: Create a new id filter with the specified list of ids.
inputPath - Variable in class org.dishevelled.bio.tools.AbstractRenameReferences
inputPath - Variable in class org.dishevelled.bio.tools.AbstractSplit: Input path, if any.
InterleavedFastqToBam - Class in org.dishevelled.bio.tools: Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
InterleavedFastqToBam(File, File, String, String, String, String, Integer, List<String>) - Constructor for class org.dishevelled.bio.tools.InterleavedFastqToBam: Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
InterleavedFastqToBam(Path, File, String, String, String, String, Integer, List<String>) - Constructor for class org.dishevelled.bio.tools.InterleavedFastqToBam: Convert DNA sequences in interleaved FASTQ format to unaligned BAM format.
InterleaveFastq - Class in org.dishevelled.bio.tools: Convert first and second DNA sequence files in FASTQ format to interleaved FASTQ format.
InterleaveFastq(File, File, File, File) - Constructor for class org.dishevelled.bio.tools.InterleaveFastq: Convert first and second DNA sequence files in FASTQ format to interleaved FASTQ format.
InterleaveFastq(Path, Path, File, File) - Constructor for class org.dishevelled.bio.tools.InterleaveFastq: Convert first and second DNA sequence files in FASTQ format to interleaved FASTQ format.
IntersectBed - Class in org.dishevelled.bio.tools: Similar to bedtools2 intersect -v.
IntersectBed(File, File, File, IntersectBed.Strategy) - Constructor for class org.dishevelled.bio.tools.IntersectBed: Similar to bedtools2 intersect -v.
IntersectBed(Path, Path, File, IntersectBed.Strategy) - Constructor for class org.dishevelled.bio.tools.IntersectBed: Similar to bedtools2 intersect -v.
intersectBed(BufferedReader, BufferedReader, PrintWriter) - Method in interface org.dishevelled.bio.tools.IntersectBed.Strategy
IntersectBed.Strategy - Interface in org.dishevelled.bio.tools: Intersect BED strategy.
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.CompressFasta
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.ExtractFasta
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.FastaToText
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.FilterFasta
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.SplitFasta
isProteinAlphabet() - Method in class org.dishevelled.bio.tools.TruncateFasta

K

KmerCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.KmerCountFilter: Create a new k-mer count filter with the specified read count.
KmerCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.KmerCountFilter: Create a new k-mer count filter with the specified read count.

L

leftPad(int) - Method in class org.dishevelled.bio.tools.AbstractSplit: Left pad the specified split index.
LengthFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterFasta.LengthFilter: Create a new length filter with the specified length.
LengthFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterFastq.LengthFilter: Create a new length filter with the specified length.
LengthFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.LengthFilter: Create a new length filter with the specified length.
LengthFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.LengthFilter: Create a new length filter with the specified length.
license() - Method in class org.dishevelled.bio.tools.About: Return the license.
LinksToCytoscapeEdges - Class in org.dishevelled.bio.tools: Convert links in GFA 1.0 format to edges.txt format for Cytoscape.
LinksToCytoscapeEdges(File, File) - Constructor for class org.dishevelled.bio.tools.LinksToCytoscapeEdges: Convert links in GFA 1.0 format to edges.txt format for Cytoscape.
LinksToCytoscapeEdges(Path, File) - Constructor for class org.dishevelled.bio.tools.LinksToCytoscapeEdges: Convert links in GFA 1.0 format to edges.txt format for Cytoscape.
LinksToPropertyGraph - Class in org.dishevelled.bio.tools: Convert links in GFA 1.0 format to property graph CSV format.
LinksToPropertyGraph(File, File) - Constructor for class org.dishevelled.bio.tools.LinksToPropertyGraph: Convert links in GFA 1.0 format to property graph CSV format.
LinksToPropertyGraph(Path, File) - Constructor for class org.dishevelled.bio.tools.LinksToPropertyGraph: Convert links in GFA 1.0 format to property graph CSV format.
ListFilesystems - Class in org.dishevelled.bio.tools: List installed filesystem providers.
ListFilesystems() - Constructor for class org.dishevelled.bio.tools.ListFilesystems

M

main(String[]) - Static method in class org.dishevelled.bio.tools.BinFastqQualityScores: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressBed: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressGaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressGfa1: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressGfa2: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressGff3: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressPaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressRgfa: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressSam: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CompressVcf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.CreateSequenceDictionary: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.DisinterleaveFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.DownsampleFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.DownsampleInterleavedFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.EnsemblVariantTableToVcf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ExportSegments: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ExtractFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ExtractFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ExtractFastqByLength: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastaToFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastaToText: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastqDescription: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastqSequenceLength: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastqToBam: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastqToFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FastqToText: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterBed: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterGaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterGfa1: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterGfa2: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterGff3: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterPaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterRgfa: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterSam: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.FilterVcf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.Gfa1ToGfa2: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.IdentifyGfa1: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.InterleavedFastqToBam: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.InterleaveFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.IntersectBed: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.LinksToCytoscapeEdges: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.LinksToPropertyGraph: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ListFilesystems: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.ReassemblePaths: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RemapDbSnp: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RemapPhaseSet: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RenameBedReferences: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RenameGff3References: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RenameReferences: Deprecated.

Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.RenameVcfReferences: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SegmentsToCytoscapeNodes: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SegmentsToPropertyGraph: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitBed: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitGaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitGff3: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitInterleavedFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitPaf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitSam: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.SplitVcf: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TextToFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TextToFastq: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.Tools: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TraversalsToCytoscapeEdges: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TraversalsToPropertyGraph: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TraversePaths: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TruncateFasta: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.TruncatePaths: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.VcfHeader: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.VcfPedigree: Main.
main(String[]) - Static method in class org.dishevelled.bio.tools.VcfSamples: Main.
MappingQualityFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGaf.MappingQualityFilter: Create a new mapping quality score filter with the specified mapping quality.
MappingQualityFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.MappingQualityFilter: Create a new mapping quality filter with the specified mapping quality.
MappingQualityFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterPaf.MappingQualityFilter: Create a new mapping quality score filter with the specified mapping quality.
MappingQualityFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.MappingQualityFilter: Create a new mapping quality filter with the specified mapping quality.
MapqFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterSam.MapqFilter: Create a new MAPQ score filter with the specified MAPQ.
MismatchCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.MismatchCountFilter: Create a new mismatch count filter with the specified mismatch count.
MismatchCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.MismatchCountFilter: Create a new mismatch count filter with the specified mismatch count.

O

org.dishevelled.bio.tools - package org.dishevelled.bio.tools: Command line tools.
outputFile - Variable in class org.dishevelled.bio.tools.AbstractRenameReferences

Q

QualFilter(double) - Constructor for class org.dishevelled.bio.tools.FilterVcf.QualFilter: Create a new quality score filter with the specified quality score.
QueryRangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGaf.QueryRangeFilter: Create a new range filter with the specified range format.
QueryRangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterPaf.QueryRangeFilter: Create a new query range filter with the specified range format.

R

RangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterBed.RangeFilter: Create a new range filter with the specified range format.
RangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGff3.RangeFilter: Create a new range filter with the specified range format.
RangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterSam.RangeFilter: Create a new range filter with the specified range format.
RangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterVcf.RangeFilter: Create a new range filter with the specified range format.
ReadCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.ReadCountFilter: Create a new read count filter with the specified read count.
ReadCountFilter(int) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.ReadCountFilter: Create a new read count filter with the specified read count.
ReassemblePaths - Class in org.dishevelled.bio.tools: Reassemble paths in GFA 1.0 format, recreating segments and overlaps fields from traversal records.
ReassemblePaths(File, File) - Constructor for class org.dishevelled.bio.tools.ReassemblePaths: Reassemble paths in GFA 1.0 format, recreating segments and overlaps fields from traversal records.
ReassemblePaths(Path, File) - Constructor for class org.dishevelled.bio.tools.ReassemblePaths: Reassemble paths in GFA 1.0 format, recreating segments and overlaps fields from traversal records.
records - Variable in class org.dishevelled.bio.tools.AbstractSplit: Split the input path after each n records, if any.
RemapDbSnp - Class in org.dishevelled.bio.tools: Remap DB Type=String flags in VCF format to DB Type=Flag and dbsnp Type=String fields.
RemapDbSnp(File, File) - Constructor for class org.dishevelled.bio.tools.RemapDbSnp: Remap DB Type=String flags in VCF format to DB Type=Flag and dbsnp Type=String fields.
RemapDbSnp(Path, File) - Constructor for class org.dishevelled.bio.tools.RemapDbSnp: Remap DB Type=String flags in VCF format to DB Type=Flag and dbsnp Type=String fields.
RemapPhaseSet - Class in org.dishevelled.bio.tools: Remap PS Type=String phase set ids in VCF format to PS Type=Integer.
RemapPhaseSet(File, File) - Constructor for class org.dishevelled.bio.tools.RemapPhaseSet: Remap Type=String PS phase set ids in VCF format to Type=Integer.
RemapPhaseSet(Path, File) - Constructor for class org.dishevelled.bio.tools.RemapPhaseSet: Remap Type=String PS phase set ids in VCF format to Type=Integer.
removeChr(String) - Static method in class org.dishevelled.bio.tools.AbstractRenameReferences: Remove "chr" from the specified reference name.
removeChr(String) - Static method in class org.dishevelled.bio.tools.RenameReferences: Deprecated.
rename(String) - Method in class org.dishevelled.bio.tools.AbstractRenameReferences: Rename the specified reference name.
rename(String) - Method in class org.dishevelled.bio.tools.RenameReferences: Deprecated.
RenameBedReferences - Class in org.dishevelled.bio.tools: Rename references in BED files.
RenameBedReferences(boolean, File, File) - Constructor for class org.dishevelled.bio.tools.RenameBedReferences: Rename references in BED files.
RenameBedReferences(boolean, Path, File) - Constructor for class org.dishevelled.bio.tools.RenameBedReferences: Rename references in BED files.
RenameGff3References - Class in org.dishevelled.bio.tools: Rename references in GFF3 files.
RenameGff3References(boolean, File, File) - Constructor for class org.dishevelled.bio.tools.RenameGff3References: Rename references in GFF3 files.
RenameGff3References(boolean, Path, File) - Constructor for class org.dishevelled.bio.tools.RenameGff3References: Rename references in GFF3 files.
RenameReferences - Class in org.dishevelled.bio.tools: Deprecated.
by RenameGff3References in version 2.1, to be removed in 3.0
RenameReferences(boolean, File, File) - Constructor for class org.dishevelled.bio.tools.RenameReferences: Deprecated.

Rename references in GFF3 files.
RenameReferences(boolean, Path, File) - Constructor for class org.dishevelled.bio.tools.RenameReferences: Deprecated.

Rename references in GFF3 files.
RenameVcfReferences - Class in org.dishevelled.bio.tools: Rename references in VCF files.
RenameVcfReferences(boolean, File, File) - Constructor for class org.dishevelled.bio.tools.RenameVcfReferences: Rename references in VCF files.
RenameVcfReferences(boolean, Path, File) - Constructor for class org.dishevelled.bio.tools.RenameVcfReferences: Rename references in VCF files.

S

ScoreFilter(double) - Constructor for class org.dishevelled.bio.tools.FilterBed.ScoreFilter: Create a new score filter with the specified score.
ScoreFilter(double) - Constructor for class org.dishevelled.bio.tools.FilterGff3.ScoreFilter: Create a new score filter with the specified score.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterBed.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterFasta.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterFastq.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGaf.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGfa1.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGfa2.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterGff3.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterPaf.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterRgfa.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterSam.ScriptFilter: Create a new script filter with the specified script.
ScriptFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterVcf.ScriptFilter: Create a new script filter with the specified script.
SegmentFilter() - Constructor for class org.dishevelled.bio.tools.FilterGfa1.SegmentFilter
SegmentFilter() - Constructor for class org.dishevelled.bio.tools.FilterRgfa.SegmentFilter
SegmentsToCytoscapeNodes - Class in org.dishevelled.bio.tools: Convert segments in GFA 1.0 format to nodes.txt format for Cytoscape.
SegmentsToCytoscapeNodes(File, File) - Constructor for class org.dishevelled.bio.tools.SegmentsToCytoscapeNodes: Convert segments in GFA 1.0 format to nodes.txt format for Cytoscape.
SegmentsToCytoscapeNodes(Path, File) - Constructor for class org.dishevelled.bio.tools.SegmentsToCytoscapeNodes: Convert segments in GFA 1.0 format to nodes.txt format for Cytoscape.
SegmentsToPropertyGraph - Class in org.dishevelled.bio.tools: Convert segments in GFA 1.0 format to property graph CSV format.
SegmentsToPropertyGraph(File, File) - Constructor for class org.dishevelled.bio.tools.SegmentsToPropertyGraph: Convert segments in GFA 1.0 format to property graph CSV format.
SegmentsToPropertyGraph(Path, File) - Constructor for class org.dishevelled.bio.tools.SegmentsToPropertyGraph: Convert segments in GFA 1.0 format to property graph CSV format.
SplitBed - Class in org.dishevelled.bio.tools: Split BED files.
SplitBed(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitBed: Split BED files.
SplitBed(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitBed: Split BED files.
SplitBed(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitBed: Split BED files.
SplitBed(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitBed: Split BED files.
SplitFasta - Class in org.dishevelled.bio.tools: Split FASTA files.
SplitFasta(File, Long, Long, String, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFasta(Path, Long, Long, String, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFasta(File, Long, Long, String, int, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFasta(Path, Long, Long, String, int, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFasta(File, String, Long, Long, String, int, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFasta(Path, String, Long, Long, String, int, String, int) - Constructor for class org.dishevelled.bio.tools.SplitFasta: Split FASTA files.
SplitFastq - Class in org.dishevelled.bio.tools: Split FASTQ files.
SplitFastq(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitFastq: Split FASTQ files.
SplitFastq(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitFastq: Split FASTQ files.
SplitFastq(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitFastq: Split FASTQ files.
SplitFastq(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitFastq: Split FASTQ files.
SplitGaf - Class in org.dishevelled.bio.tools: Split GAF files.
SplitGaf(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitGaf: Split GAF files.
SplitGaf(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitGaf: Split GAF files.
SplitGaf(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitGaf: Split GAF files.
SplitGaf(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitGaf: Split GAF files.
SplitGff3 - Class in org.dishevelled.bio.tools: Split GFF3 files.
SplitGff3(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitGff3: Split GFF3 files.
SplitGff3(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitGff3: Split GFF3 files.
SplitGff3(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitGff3: Split GFF3 files.
SplitGff3(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitGff3: Split GFF3 files.
SplitInterleavedFastq - Class in org.dishevelled.bio.tools: Split interleaved FASTQ files.
SplitInterleavedFastq(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitInterleavedFastq: Split interleaved FASTQ files.
SplitInterleavedFastq(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitInterleavedFastq: Split interleaved FASTQ files.
SplitInterleavedFastq(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitInterleavedFastq: Split interleaved FASTQ files.
SplitInterleavedFastq(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitInterleavedFastq: Split interleaved FASTQ files.
SplitPaf - Class in org.dishevelled.bio.tools: Split PAF files.
SplitPaf(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitPaf: Split PAF files.
SplitPaf(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitPaf: Split PAF files.
SplitPaf(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitPaf: Split PAF files.
SplitPaf(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitPaf: Split PAF files.
SplitSam - Class in org.dishevelled.bio.tools: Split SAM files.
SplitSam(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitSam: Split SAM files.
SplitSam(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitSam: Split SAM files.
SplitSam(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitSam: Split SAM files.
SplitSam(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitSam: Split SAM files.
SplitVcf - Class in org.dishevelled.bio.tools: Split VCF files.
SplitVcf(File, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitVcf: Split VCF files.
SplitVcf(Path, Long, Long, String, String) - Constructor for class org.dishevelled.bio.tools.SplitVcf: Split VCF files.
SplitVcf(File, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitVcf: Split VCF files.
SplitVcf(Path, Long, Long, String, int, String) - Constructor for class org.dishevelled.bio.tools.SplitVcf: Split VCF files.

T

TargetRangeFilter(String) - Constructor for class org.dishevelled.bio.tools.FilterPaf.TargetRangeFilter: Create a new target range filter with the specified range format.
TextToFasta - Class in org.dishevelled.bio.tools: Convert DNA or protein sequences in tab-separated values (tsv) text format to FASTA format.
TextToFasta(Path, File, String, int) - Constructor for class org.dishevelled.bio.tools.TextToFasta: Convert DNA or protein sequences in tab-separated values (tsv) text format to FASTA format.
TextToFastq - Class in org.dishevelled.bio.tools: Convert DNA sequences in tab-separated values (tsv) text format to FASTQ format.
TextToFastq(File, File) - Constructor for class org.dishevelled.bio.tools.TextToFastq: Convert DNA sequences in tab-separated values (tsv) text format to FASTQ format.
TextToFastq(Path, File) - Constructor for class org.dishevelled.bio.tools.TextToFastq: Convert DNA sequences in tab-separated values (tsv) text format to FASTQ format.
toBytes(String) - Static method in class org.dishevelled.bio.tools.AbstractSplit: Parse the specified byte string (e.g.
toGfa2Orientation(Orientation) - Static method in class org.dishevelled.bio.tools.Gfa1ToGfa2
toGfa2Reference(Reference) - Static method in class org.dishevelled.bio.tools.Gfa1ToGfa2
toGfa2References(List<Reference>) - Static method in class org.dishevelled.bio.tools.Gfa1ToGfa2
Tools - Class in org.dishevelled.bio.tools: Command line tools.
Tools(String[], SortedMap<String, Tools.Command>) - Constructor for class org.dishevelled.bio.tools.Tools: Create a new tools callable with the specified map of commands keyed by name and array of arguments.
Tools.Command - Class in org.dishevelled.bio.tools: Command.
toReadGroup() - Method in class org.dishevelled.bio.tools.WithReadGroup: Create and return a new read group.
toReadGroupOpt() - Method in class org.dishevelled.bio.tools.WithReadGroup: Create and return an optional wrapping the read group, if any.
toString() - Method in class org.dishevelled.bio.tools.About
TraversalsToCytoscapeEdges - Class in org.dishevelled.bio.tools: Convert traversals in GFA 1.0 format to edges.txt format for Cytoscape.
TraversalsToCytoscapeEdges(File, File) - Constructor for class org.dishevelled.bio.tools.TraversalsToCytoscapeEdges: Convert traversals in GFA 1.0 format to edges.txt format for Cytoscape.
TraversalsToCytoscapeEdges(Path, File) - Constructor for class org.dishevelled.bio.tools.TraversalsToCytoscapeEdges: Convert traversals in GFA 1.0 format to edges.txt format for Cytoscape.
TraversalsToPropertyGraph - Class in org.dishevelled.bio.tools: Convert traversals in GFA 1.0 format to property graph CSV format.
TraversalsToPropertyGraph(File, File) - Constructor for class org.dishevelled.bio.tools.TraversalsToPropertyGraph: Convert traversals in GFA 1.0 format to property graph CSV format.
TraversalsToPropertyGraph(Path, File) - Constructor for class org.dishevelled.bio.tools.TraversalsToPropertyGraph: Convert traversals in GFA 1.0 format to property graph CSV format.
TraversePaths - Class in org.dishevelled.bio.tools: Traverse paths in GFA 1.0 format, creating new traversal records.
TraversePaths(File, File) - Constructor for class org.dishevelled.bio.tools.TraversePaths: Traverse paths in GFA 1.0 format, creating new traversal records.
TraversePaths(Path, File) - Constructor for class org.dishevelled.bio.tools.TraversePaths: Traverse paths in GFA 1.0 format, creating new traversal records.
TruncateFasta - Class in org.dishevelled.bio.tools: Truncate DNA or protein sequences in FASTA format.
TruncateFasta(File, File, int, int) - Constructor for class org.dishevelled.bio.tools.TruncateFasta: Truncate DNA or protein sequences in FASTA format.
TruncateFasta(Path, File, int, int) - Constructor for class org.dishevelled.bio.tools.TruncateFasta: Truncate DNA or protein sequences in FASTA format.
TruncateFasta(File, File, int, String, int) - Constructor for class org.dishevelled.bio.tools.TruncateFasta: Truncate DNA or protein sequences in FASTA format.
TruncateFasta(Path, File, int, String, int) - Constructor for class org.dishevelled.bio.tools.TruncateFasta: Truncate DNA or protein sequences in FASTA format.
TruncatePaths - Class in org.dishevelled.bio.tools: Truncate paths in GFA 1.0 format, removing segments and overlaps fields.
TruncatePaths(File, File) - Constructor for class org.dishevelled.bio.tools.TruncatePaths: Truncate paths in GFA 1.0 format, removing segments and overlaps fields.
TruncatePaths(Path, File) - Constructor for class org.dishevelled.bio.tools.TruncatePaths: Truncate paths in GFA 1.0 format, removing segments and overlaps fields.

U

usage() - Method in class org.dishevelled.bio.tools.Tools: Return the usage message.

V

VcfHeader - Class in org.dishevelled.bio.tools: Extract and validate header lines from VCF format.
VcfHeader(File, File, boolean) - Constructor for class org.dishevelled.bio.tools.VcfHeader: Extract and validate header lines from VCF format.
VcfHeader(Path, File, boolean) - Constructor for class org.dishevelled.bio.tools.VcfHeader: Extract and validate header lines from VCF format.
VcfPedigree - Class in org.dishevelled.bio.tools: Extract a pedigree from VCF format.
VcfPedigree(File, File) - Constructor for class org.dishevelled.bio.tools.VcfPedigree: Extract a pedigree from VCF format.
VcfPedigree(Path, File) - Constructor for class org.dishevelled.bio.tools.VcfPedigree: Extract a pedigree from VCF format.
VcfSamples - Class in org.dishevelled.bio.tools: Extract samples from VCF format.
VcfSamples(File, File) - Constructor for class org.dishevelled.bio.tools.VcfSamples: Extract samples from VCF format.
VcfSamples(Path, File) - Constructor for class org.dishevelled.bio.tools.VcfSamples: Extract samples from VCF format.
version() - Method in class org.dishevelled.bio.tools.About: Return the version.

W

WithReadGroup - Class in org.dishevelled.bio.tools: Abstract callable with read group.
WithReadGroup(String, String, String, String, Integer, List<String>) - Constructor for class org.dishevelled.bio.tools.WithReadGroup: Create a new callable with a read group with the specified annotations.
writeSequence(Sequence, int, PrintWriter) - Static method in class org.dishevelled.bio.tools.CompressFasta
writeSequence(Sequence, int, PrintWriter) - Static method in class org.dishevelled.bio.tools.ExtractFasta
writeSequence(Sequence, int, PrintWriter) - Static method in class org.dishevelled.bio.tools.FilterFasta
writeSequence(Sequence, int, PrintWriter) - Static method in class org.dishevelled.bio.tools.SplitFasta
writeSequence(Sequence, int, PrintWriter) - Static method in class org.dishevelled.bio.tools.TruncateFasta

A B C D E F G I K L M O Q R S T U V W