Download jillion JAR 5.3.2 with all dependencies

An open source genomics software library written in Java to support sequence and assembly analysis

Files of the artifact jillion version 5.3.2 from the group org.jcvi.jillion.

Artifact jillion
Group org.jcvi.jillion
Version 5.3.2
Last update 24. September 2019
Tags: open software support source sequence assembly written library java genomics analysis
Organization J. Craig Venter Institute
URL http://jillion.sourceforge.net
License GNU LGPL 2.1 or later
Dependencies amount 1
Dependencies annotations,
There are maybe transitive dependencies!

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Source code of jillion version 5.3.2

META-INF

META-INF.META-INF.MANIFEST.MF

org.jcvi.jillion.align

org.jcvi.jillion.align.org.jcvi.jillion.align.AbstractSubstitutionMatrixFileParser

org.jcvi.jillion.align.org.jcvi.jillion.align.AminoAcidSubstitutionMatrix

org.jcvi.jillion.align.org.jcvi.jillion.align.AminoAcidSubstitutionMatrixFileParser

org.jcvi.jillion.align.org.jcvi.jillion.align.BlosumMatrices

org.jcvi.jillion.align.org.jcvi.jillion.align.NucleotidePropertyFileScoringMatrixParser

org.jcvi.jillion.align.org.jcvi.jillion.align.NucleotideSequenceAlignment

org.jcvi.jillion.align.org.jcvi.jillion.align.NucleotideSubstitutionMatrices

org.jcvi.jillion.align.org.jcvi.jillion.align.NucleotideSubstitutionMatrix

org.jcvi.jillion.align.org.jcvi.jillion.align.NucleotideSubstitutionMatrixBuilder

org.jcvi.jillion.align.org.jcvi.jillion.align.ProteinSequenceAlignment

org.jcvi.jillion.align.org.jcvi.jillion.align.SequenceAlignment

org.jcvi.jillion.align.org.jcvi.jillion.align.SubstitutionMatrix

org.jcvi.jillion.align.org.jcvi.jillion.align.blosum30.matrix

org.jcvi.jillion.align.org.jcvi.jillion.align.blosum40.matrix

org.jcvi.jillion.align.org.jcvi.jillion.align.blosum50.matrix

org.jcvi.jillion.align.org.jcvi.jillion.align.blosum62.matrix

org.jcvi.jillion.align.org.jcvi.jillion.align.blosum90.matrix

org.jcvi.jillion.align.exonerate

org.jcvi.jillion.align.exonerate.org.jcvi.jillion.align.exonerate.Exonerate

org.jcvi.jillion.align.exonerate.org.jcvi.jillion.align.exonerate.Exonerate2

org.jcvi.jillion.align.exonerate.org.jcvi.jillion.align.exonerate.package-info

org.jcvi.jillion.align.exonerate.vulgar

org.jcvi.jillion.align.exonerate.vulgar.org.jcvi.jillion.align.exonerate.vulgar.VulgarElement

org.jcvi.jillion.align.exonerate.vulgar.org.jcvi.jillion.align.exonerate.vulgar.VulgarOperation

org.jcvi.jillion.align.exonerate.vulgar.org.jcvi.jillion.align.exonerate.vulgar.VulgarProtein2Genome

org.jcvi.jillion.align.exonerate.vulgar.org.jcvi.jillion.align.exonerate.vulgar.VulgarProtein2Genome2

org.jcvi.jillion.align.exonerate.vulgar.org.jcvi.jillion.align.exonerate.vulgar.package-info

org.jcvi.jillion.align

org.jcvi.jillion.align.org.jcvi.jillion.align.nuc4.4.matrix

org.jcvi.jillion.align.org.jcvi.jillion.align.package-info

org.jcvi.jillion.align.pairwise

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.AbstractNeedlemanWunschAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.AbstractPairwiseAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.AbstractPairwiseSequenceAlignment

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.AbstractSmithWatermanAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.NucleotideNeedlemanWunschAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.NucleotidePairwiseSequenceAlignment

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.NucleotidePairwiseSequenceAlignmentImpl

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.NucleotideSmithWatermanAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.PairwiseAlignmentBuilder

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.PairwiseSequenceAlignment

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.PairwiseSequenceAlignmentWrapper

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.ProteinNeedlemanWunschAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.ProteinPairwiseSequenceAlignment

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.ProteinPairwiseSequenceAlignmentImpl

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.ProteinSmithWatermanAligner

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.ResiduePairwiseStrategy

org.jcvi.jillion.align.pairwise.org.jcvi.jillion.align.pairwise.package-info

org.jcvi.jillion.assembly

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AbstractAssemblyTransformer

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AbstractContigBuilder

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AssembledRead

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AssembledReadBuilder

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AssemblyTransformationService

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AssemblyTransformer

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.AssemblyUtil

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.Contig

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ContigBuilder

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ContigDataStore

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ContigDataStoreTransfomationService

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.DefaultPlacedContig

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.DefaultScaffold

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.DefaultScaffoldDataStore

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.GappedReferenceBuilder

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.PlacedContig

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ReadInfo

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.Scaffold

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ScaffoldBuilder

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ScaffoldDataStore

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.ScaffoldDataStoreBuilder

org.jcvi.jillion.assembly.ca.asm

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AbstractAsmContigBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AbstractAsmUnitigBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmAssembledRead

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmAssembledReadBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmContig

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmContigBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmContigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmContigVisitor

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmFileContigDataStoreBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmFileParser

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmFileUnitigDataStoreBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmParser

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmScaffoldVisitor

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmUnitig

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmUnitigBuilder

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmUnitigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmUnitigVisitor

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmUtil

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.AsmVisitor

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.DefaultAsmAssembledRead

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.DefaultAsmContig

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.DefaultAsmContigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.DefaultAsmUnitig

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.DefaultAsmUnitigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.IndexedAsmFileContigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.IndexedAsmFileUnitigDataStore

org.jcvi.jillion.assembly.ca.asm.org.jcvi.jillion.assembly.ca.asm.package-info

org.jcvi.jillion.assembly.ca.frg

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.AbstractFragmentDataStore

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.DefaultFragment

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.DefaultFragmentDataStore

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.DefaultLibrary

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.Distance

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.Fragment

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.FragmentDataStore

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.FragmentUtil

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.Frg2Parser

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.Frg2Visitor

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.IndexedFragmentDataStore

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.Library

org.jcvi.jillion.assembly.ca.frg.org.jcvi.jillion.assembly.ca.frg.MateOrientation

org.jcvi.jillion.assembly.ca

org.jcvi.jillion.assembly.ca.org.jcvi.jillion.assembly.ca.package-info

org.jcvi.jillion.assembly.clc.cas

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.AbstractAlignedReadCasVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.AbstractCasFileVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.AbstractReadCasVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignment

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignmentRegion

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignmentRegionType

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignmentScore

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignmentScoreBuilder

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasAlignmentType

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasColorSpaceAlignmentScore

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasContigPair

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasFileInfo

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasFileInfoValidator

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasFileParser

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasFileVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasFileVisitorAdapter

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasGappedReferenceDataStore

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasGappedReferenceDataStoreBuilderVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasMatch

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasMatchVisitor

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasMatchVisitorAdapter

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasParser

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasReferenceDescription

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasScoreType

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasScoringScheme

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasUtil

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.CasValidator

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignment

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignmentRegion

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignmentScore

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasColorSpaceAlignmentScore

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasFileInfo

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasMatch

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasReferenceDescription

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.DefaultCasScoringScheme

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.PhaseChangeCasAlignmentRegion

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.ReAlignReads

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.ReadFileType

org.jcvi.jillion.assembly.clc.cas.consed

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.Cas2Consed

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.ChromatDirFastaConsedPhdAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.FastaConsedPhdAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.FastqConsedPhdAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.FlowgramConsedPhdAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.PhdReadRecord

org.jcvi.jillion.assembly.clc.cas.consed.org.jcvi.jillion.assembly.clc.cas.consed.QualFastaConsedPhdAdaptedIterator

org.jcvi.jillion.assembly.clc.cas

org.jcvi.jillion.assembly.clc.cas.org.jcvi.jillion.assembly.clc.cas.package-info

org.jcvi.jillion.assembly.clc.cas.read

org.jcvi.jillion.assembly.clc.cas.read.org.jcvi.jillion.assembly.clc.cas.read.CasPlacedRead

org.jcvi.jillion.assembly.clc.cas.read.org.jcvi.jillion.assembly.clc.cas.read.DefaultCasPlacedRead

org.jcvi.jillion.assembly.clc.cas.transform

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.CasFileTransformationService

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.ChromatDirFastaReadDataAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.FastaReadDataAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.FastqReadDatadAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.FlowgramReadDataAdaptedIterator

org.jcvi.jillion.assembly.clc.cas.transform.org.jcvi.jillion.assembly.clc.cas.transform.ReadData

org.jcvi.jillion.assembly.consed

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.AceAssemblyTransformerPostProcessor

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.ConsedAssemblyTransformerBuilder

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.ConsedUtil

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.IndividualPhdConsedTransformerHelper

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.PhdBallConsedTransformerHelper

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.PhdConsedTransformerHelper

org.jcvi.jillion.assembly.consed.ace

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceConsensusTagVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceContigBuilderVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceContigReadVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceContigVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceFileVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractAceFileWriter

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractDefaultAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AbstractDefaultPlacedAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceAssembledRead

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceAssembledReadAdapter

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceAssembledReadBuilder

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceBaseSegment

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceConsensusTagVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceContig

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceContigBuilder

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceContigReadVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceContigVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceContigVisitorAdapter

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileDataStore

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileDataStoreBuilder

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileParser

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileUtil

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileVisitorCallback

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileWriter

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceFileWriterBuilder

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceParser

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.AlignedReadInfo

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.BaseSegmentUtil

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.ConsedConsensusQualityComputer

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.ConsensusAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.ConsensusAceTagBuilder

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.DefaultAceAssembledRead

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.DefaultAceBaseSegment

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.DefaultAceFileDataStore

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.HighLowAceContigPhdDatastore

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.HighLowPhdAceContigVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.IndexedAceFileDataStore

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.LargeAceFileDataStore

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.MultiAceFileVisitorAdapter

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.MultipleAceContigReadVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.MultipleAceContigVisitor

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.PhdInfo

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.RangeableAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.ReadAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.WholeAssemblyAceTag

org.jcvi.jillion.assembly.consed.ace.org.jcvi.jillion.assembly.consed.ace.package-info

org.jcvi.jillion.assembly.consed.nav

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.AbstractNavigationElement

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.ConsedNavigationParser

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.ConsedNavigationVisitor

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.ConsedNavigationWriter

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.ConsensusNavigationElement

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.NavigationElement

org.jcvi.jillion.assembly.consed.nav.org.jcvi.jillion.assembly.consed.nav.ReadNavigationElement

org.jcvi.jillion.assembly.consed

org.jcvi.jillion.assembly.consed.org.jcvi.jillion.assembly.consed.package-info

org.jcvi.jillion.assembly.consed.phd

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.AbstractPhdBallVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.AbstractPhdReadTagVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.AbstractPhdVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.ArtificialPhd

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.DefaultPhd

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.DefaultPhdDataStore

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.DefaultPhdReadTag

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.DefaultPhdWholeReadItem

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.IndexedPhdDataStore

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.LargePhdballDataStore

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.Phd

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallFileParser

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallIdIterator

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallIterator

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallParser

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallVisitorCallback

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBallWriter

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdBuilder

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdDataStore

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdDirDataStore

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdFileDataStoreBuilder

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdReadTag

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdReadTagVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdUtil

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdWholeReadItem

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdWholeReadItemVisitor

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.PhdWriter

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.ReadPhdFileFilter

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.SinglePhdWriter

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.TraceDirPhdDataStoreBuilder

org.jcvi.jillion.assembly.consed.phd.org.jcvi.jillion.assembly.consed.phd.package-info

org.jcvi.jillion.assembly.consed.transform

org.jcvi.jillion.assembly.consed.transform.org.jcvi.jillion.assembly.consed.transform.ConsedTransformationService

org.jcvi.jillion.assembly

org.jcvi.jillion.assembly.org.jcvi.jillion.assembly.package-info

org.jcvi.jillion.assembly.tigr.contig

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.AbstractTigrContigBuilderVisitor

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.CtgContigDataStore

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.DefaultTigrContigFileDataStore

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.IndexedTigrContigFileDataStore

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.LargeTigrContigFileDataStore

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContig

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigBuilder

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigDataStore

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigFileContigIterator

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigFileDataStoreBuilder

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigFileParser

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigFileVisitor

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigFileWriter

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigParser

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigRead

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigReadBuilder

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigReadVisitor

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.TigrContigVisitor

org.jcvi.jillion.assembly.tigr.contig.org.jcvi.jillion.assembly.tigr.contig.package-info

org.jcvi.jillion.assembly.tigr

org.jcvi.jillion.assembly.tigr.org.jcvi.jillion.assembly.tigr.package-info

org.jcvi.jillion.assembly.tigr.tasm

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.AbstractTasmContigBuilderVisitor

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.DefaultTasmAssembledRead

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.DefaultTasmFileContigDataStore

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.IndexedTasmFileDataStore

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.LargeTasmContigFileDataStore

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledRead

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledReadAdapter

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledReadBuilder

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContig

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigAttribute

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigBuilder

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigDataStore

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigFileContigIterator

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigFileDataStoreBuilder

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigReadVisitor

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmContigVisitor

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmFileParser

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmFileWriterBuilder

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmFileWriterUtil

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmParser

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmReadAttribute

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmUtil

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmVisitor

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.TasmWriter

org.jcvi.jillion.assembly.tigr.tasm.org.jcvi.jillion.assembly.tigr.tasm.package-info

org.jcvi.jillion.assembly.util

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.AbstractCoverageMapBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.ContigCoverageMapBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMap

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMapBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMapCollectors

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMapFactory

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMapStats

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageMapStatsCollector

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageRegion

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageRegionBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.CoverageStatsCombiner

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.DefaultCoverageRegion

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.GapQualityValueStrategy

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.ReadFilter

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.Slice

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceCombiner

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceElement

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceMap

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceMapBuilder

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.SliceMapCollector

org.jcvi.jillion.assembly.util.consensus

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.AbstractChurchillWatermanConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.AcgtnConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ChurchillWatermanConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConicConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusCollectors

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusCombiner

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusProbabilities

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusResult

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.ConsensusUtil

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.DefaultConsensusResult

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.MostFrequentBasecallConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.NextGenReferenceConsensusRecaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.NoAmbiguityConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.TigrAnnotationConsensusCaller

org.jcvi.jillion.assembly.util.consensus.org.jcvi.jillion.assembly.util.consensus.package-info

org.jcvi.jillion.assembly.util

org.jcvi.jillion.assembly.util.org.jcvi.jillion.assembly.util.package-info

org.jcvi.jillion.assembly.util.slice

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.CodonSliceMapBuilder

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.SingleNucleotideSlice

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.SingleNucleotideSliceElement

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.SingleNucleotideSliceMap

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSlice

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSliceElement

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSliceMap

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthSlice

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthSliceElement

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.VariableWidthSliceMap

org.jcvi.jillion.assembly.util.slice.org.jcvi.jillion.assembly.util.slice.package-info

org.jcvi.jillion.core

org.jcvi.jillion.core.org.jcvi.jillion.core.Defline

org.jcvi.jillion.core.org.jcvi.jillion.core.DeflineImpl

org.jcvi.jillion.core.org.jcvi.jillion.core.DirectedRange

org.jcvi.jillion.core.org.jcvi.jillion.core.Direction

org.jcvi.jillion.core.org.jcvi.jillion.core.Range

org.jcvi.jillion.core.org.jcvi.jillion.core.Rangeable

org.jcvi.jillion.core.org.jcvi.jillion.core.Ranges

org.jcvi.jillion.core.org.jcvi.jillion.core.Sequence

org.jcvi.jillion.core.org.jcvi.jillion.core.SequenceBuilder

org.jcvi.jillion.core.datastore

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStore

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreClosedException

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreEntry

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreException

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreFilter

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreFilters

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreProviderHint

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.DataStoreUtil

org.jcvi.jillion.core.datastore.org.jcvi.jillion.core.datastore.package-info

org.jcvi.jillion.core.io

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.AbstractFileInputStreamSupplier

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.BasicZipInputStreamSupplier

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.BufferSize

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.FileUtil

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.FileVisitor

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.GZipInputStreamSupplier

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.IOUtil

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.InputStreamSupplier

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.OutputStreams

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.PushBackBufferedReader

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.RawFileInputStreamSupplier

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.SubLengthInputStream

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.TextFileVisitor

org.jcvi.jillion.core.io.org.jcvi.jillion.core.io.package-info

org.jcvi.jillion.core

org.jcvi.jillion.core.org.jcvi.jillion.core.package-info

org.jcvi.jillion.core.pos

org.jcvi.jillion.core.pos.org.jcvi.jillion.core.pos.DefaultPositionCodec

org.jcvi.jillion.core.pos.org.jcvi.jillion.core.pos.DefaultPositionSequence

org.jcvi.jillion.core.pos.org.jcvi.jillion.core.pos.Position

org.jcvi.jillion.core.pos.org.jcvi.jillion.core.pos.PositionSequence

org.jcvi.jillion.core.pos.org.jcvi.jillion.core.pos.PositionSequenceBuilder

org.jcvi.jillion.core.qual

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.DefaultQualitySymbolCodec

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.EncodedQualitySequence

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.PhredQuality

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.QualitySequence

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.QualitySequenceBuilder

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.QualitySequenceDataStore

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.QualitySymbolCodec

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.RunLengthEncodedQualityCodec

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.RunLengthEncodedQualitySequence

org.jcvi.jillion.core.qual.org.jcvi.jillion.core.qual.package-info

org.jcvi.jillion.core.residue

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.Frame

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.Kmer

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.KmerSpliterator

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.Residue

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.ResidueSequence

org.jcvi.jillion.core.residue.org.jcvi.jillion.core.residue.ResidueSequenceBuilder

org.jcvi.jillion.core.residue.aa

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.AbstractProteinSequence

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.AminoAcid

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.AminoAcidCodec

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.Codon

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.CompactProteinSequence

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.CompactProteinSequenceCodec

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.IupacTranslationTables

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.ProteinSequence

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.ProteinSequenceBuilder

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.ProteinSequenceDataStore

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.TranslationTable

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.TranslationVisitor

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.UnCompressedGappedProteinSequence

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.UnCompressedUngappedProteinSequence

org.jcvi.jillion.core.residue.aa.org.jcvi.jillion.core.residue.aa.UngappedProteinSequence

org.jcvi.jillion.core.residue.nt

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.AbstractNucleotideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.AbstractTwoBitEncodedNucleotideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.AcgtGapNucleotideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.AcgtnNucloetideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.BasicNucleotideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.DefaultNucleotideSequence

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.DefaultReferenceEncodedNucleotideSequence

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.Nucleotide

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.NucleotideCodec

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.NucleotideSequence

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.NucleotideSequenceBuilder

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.NucleotideSequenceDataStore

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.NucleotideSequencePermuter

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.ReferenceMappedNucleotideSequence

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.SimpleNucleotideSequence

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.Triplet

org.jcvi.jillion.core.residue.nt.org.jcvi.jillion.core.residue.nt.UandTNucleotideCodec

org.jcvi.jillion.core.util

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.Builder

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.DateUtil

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.FileIterator

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.GenomeStatistics

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.JillionCollectors

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.JoinedStringBuilder

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.MapUtil

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.MapValueComparator

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.MemoizedSupplier

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.MultipleFileFilter

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.MultipleWrapper

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.ObjectsUtil

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.Pair

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.SingleThreadAdder

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.ThrowingStream

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.ThrowingStreamImpl

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.UnsignedByteArray

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.UnsignedIntArray

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.UnsignedShortArray

org.jcvi.jillion.core.util.iter

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.ArrayIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.ChainedIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.ChainedIteratorOfSuppliers

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.ChainedStreamingIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.ChainedStreamingIteratorFromSuppliers

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.IteratorUtil

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.PeekableIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.PeekableStreamingIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.RollOverListIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.SingleElementIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.StreamingIterator

org.jcvi.jillion.core.util.iter.org.jcvi.jillion.core.util.iter.StreamingIteratorAdapter

org.jcvi.jillion.core.util

org.jcvi.jillion.core.util.org.jcvi.jillion.core.util.package-info

org.jcvi.jillion.core.util.streams

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingBiConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingFunction

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIndexedConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedBooleanConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedByteConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedCharConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedIntConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedLongConsumer

org.jcvi.jillion.core.util.streams.org.jcvi.jillion.core.util.streams.ThrowingIntIndexedShortConsumer

org.jcvi.jillion.experimental.align

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnFileParser

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnFileWriter

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnGroupVisitor

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnParser

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnUtil

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnVisitor

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.AlnWriter

org.jcvi.jillion.experimental.align.org.jcvi.jillion.experimental.align.GappedNucleotideAlignmentDataStore

org.jcvi.jillion.experimental.align.blast

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.BlastHit

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.BlastHitImpl

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.BlastParser

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.BlastVisitor

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.Hsp

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.HspBuilder

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.TabularBlastParser

org.jcvi.jillion.experimental.align.blast.org.jcvi.jillion.experimental.align.blast.XmlFileBlastParser

org.jcvi.jillion.experimental.align.blast.btab

org.jcvi.jillion.experimental.align.blast.btab.org.jcvi.jillion.experimental.align.blast.btab.BtabWriter

org.jcvi.jillion.experimental.align.blast.btab.org.jcvi.jillion.experimental.align.blast.btab.BtabWriterBuilder

org.jcvi.jillion.experimental.align.blast.btab.org.jcvi.jillion.experimental.align.blast.btab.package-info

org.jcvi.jillion.experimental.assembly.agp

org.jcvi.jillion.experimental.assembly.agp.org.jcvi.jillion.experimental.assembly.agp.AgpFileVisitor

org.jcvi.jillion.experimental.assembly.agp.org.jcvi.jillion.experimental.assembly.agp.AgpParser

org.jcvi.jillion.experimental.assembly.agp.org.jcvi.jillion.experimental.assembly.agp.AgpWriter

org.jcvi.jillion.experimental.assembly.agp.org.jcvi.jillion.experimental.assembly.agp.DefaultAgpScaffoldDataStore

org.jcvi.jillion.experimental.assembly.agp.org.jcvi.jillion.experimental.assembly.agp.ScaffoldDataStoreBuilderAgpVisitor

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveConformation

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveMetaData

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveType

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveWriter

org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveWriterBuilder

org.jcvi.jillion.experimental.plate

org.jcvi.jillion.experimental.plate.org.jcvi.jillion.experimental.plate.PlateFormat

org.jcvi.jillion.experimental.plate.org.jcvi.jillion.experimental.plate.PlatePopulator

org.jcvi.jillion.experimental.plate.org.jcvi.jillion.experimental.plate.Well

org.jcvi.jillion.experimental.primer

org.jcvi.jillion.experimental.primer.org.jcvi.jillion.experimental.primer.OptimalMeltingTemperatureEstimator

org.jcvi.jillion.experimental.primer.org.jcvi.jillion.experimental.primer.PrimerDetector

org.jcvi.jillion.experimental.primer.org.jcvi.jillion.experimental.primer.PrimerUtil

org.jcvi.jillion.experimental.primer.org.jcvi.jillion.experimental.primer.SaltCorrectionStrategy

org.jcvi.jillion.experimental.primer.org.jcvi.jillion.experimental.primer.package-info

org.jcvi.jillion.experimental.trace.archive2

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.DefaultTraceArchiveInfo

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.DefaultTraceArchiveRecord

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceArchiveInfo

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceArchiveRecord

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceArchiveRecordBuilder

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceArchiveWriter

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceInfoField

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.TraceInfoWriterUtil

org.jcvi.jillion.experimental.trace.archive2.org.jcvi.jillion.experimental.trace.archive2.XmlTraceArchiveInfoFactory

org.jcvi.jillion.fasta

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.AbstractFastaRecordVisitor

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaCollectors

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaDataStore

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaFileParser

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaParser

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaRecord

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaRecordVisitor

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaVisitor

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaVisitorCallback

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaWriter

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.FastaWriterAdapterImpl

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.SplitFastaWriter

org.jcvi.jillion.fasta.aa

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.AbstractProteinFastaRecordVisitor

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaDataStore

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaFileDataStore

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaFileDataStoreBuilder

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaRecord

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaRecordBuilder

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaWriter

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.ProteinFastaWriterBuilder

org.jcvi.jillion.fasta.aa.org.jcvi.jillion.fasta.aa.package-info

org.jcvi.jillion.fasta.nt

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.AbstractNucleotideFastaRecordVisitor

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.CommentedNucleotideSequenceFastaRecord

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.DefaultNucleotideFastaFileDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.FaiNucleotideFastaFileDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.FaiNucleotideFastaWriter

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.FaiNucleotideWriterBuilder

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.IndexedNucleotideSequenceFastaFileDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.LargeNucleotideSequenceFastaFileDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.LargeNucleotideSequenceFastaIterator

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaFileDataStore

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaFileDataStoreBuilder

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaFileReader

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaRecord

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaRecordBuilder

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaWriter

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.NucleotideFastaWriterBuilder

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.UnCommentedNucleotideSequenceFastaRecord

org.jcvi.jillion.fasta.nt.org.jcvi.jillion.fasta.nt.package-info

org.jcvi.jillion.fasta

org.jcvi.jillion.fasta.org.jcvi.jillion.fasta.package-info

org.jcvi.jillion.fasta.pos

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.AbstractPositionSequenceFastaRecordVisitor

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.DefaultPositionFastaFileDataStore

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.LargePositionFastaFileDataStore

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.LargePositionFastaIterator

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionFastaDataStore

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionFastaFileDataStoreBuilder

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionFastaRecord

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionFastaWriter

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionFastaWriterBuilder

org.jcvi.jillion.fasta.pos.org.jcvi.jillion.fasta.pos.PositionSequenceDataStore

org.jcvi.jillion.fasta.qual

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.AbstractQualityFastaRecordVisitor

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.CommentedQualityFastaRecord

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.DefaultQualityFastaFileDataStore

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaDataStore

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaFileDataStoreBuilder

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaRecord

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaRecordBuilder

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaWriter

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.QualityFastaWriterBuilder

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.UncommentedQualityFastaRecord

org.jcvi.jillion.fasta.qual.org.jcvi.jillion.fasta.qual.package-info

org.jcvi.jillion.internal

org.jcvi.jillion.internal.org.jcvi.jillion.internal.ResourceHelper

org.jcvi.jillion.internal.align

org.jcvi.jillion.internal.align.org.jcvi.jillion.internal.align.AbstractSequenceAlignmentBuilder

org.jcvi.jillion.internal.align.org.jcvi.jillion.internal.align.NucleotideSequenceAlignmentBuilder

org.jcvi.jillion.internal.align.org.jcvi.jillion.internal.align.ProteinSequenceAlignmentBuilder

org.jcvi.jillion.internal.align.org.jcvi.jillion.internal.align.SequenceAlignmentBuilder

org.jcvi.jillion.internal.assembly

org.jcvi.jillion.internal.assembly.org.jcvi.jillion.internal.assembly.DefaultAssembledRead

org.jcvi.jillion.internal.assembly.org.jcvi.jillion.internal.assembly.DefaultContig

org.jcvi.jillion.internal.assembly.util

org.jcvi.jillion.internal.assembly.util.org.jcvi.jillion.internal.assembly.util.CompactedSliceElement

org.jcvi.jillion.internal.assembly.util.org.jcvi.jillion.internal.assembly.util.CompactedSliceMap

org.jcvi.jillion.internal.assembly.util.org.jcvi.jillion.internal.assembly.util.ConsensusCompactedSlice

org.jcvi.jillion.internal.assembly.util.org.jcvi.jillion.internal.assembly.util.NoConsensusCompactedSlice

org.jcvi.jillion.internal.core

org.jcvi.jillion.internal.core.org.jcvi.jillion.internal.core.EncodedSequence

org.jcvi.jillion.internal.core.org.jcvi.jillion.internal.core.GlyphCodec

org.jcvi.jillion.internal.core.datastore

org.jcvi.jillion.internal.core.datastore.org.jcvi.jillion.internal.core.datastore.AbstractDataStore

org.jcvi.jillion.internal.core.datastore.org.jcvi.jillion.internal.core.datastore.AbstractMapBackedDataStore

org.jcvi.jillion.internal.core.datastore.org.jcvi.jillion.internal.core.datastore.DataStoreIterator

org.jcvi.jillion.internal.core.datastore.org.jcvi.jillion.internal.core.datastore.DataStoreStreamingIterator

org.jcvi.jillion.internal.core.io

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.BlockingAccumulator

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.ByteBufferInputStream

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.LineParser

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.MagicNumberInputStream

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.OpenAwareInputStream

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.OutputStreamFactory

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.PositionlessLineParser

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.RandomAccessFileInputStream

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.StreamUtil

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.TextLineParser

org.jcvi.jillion.internal.core.io.org.jcvi.jillion.internal.core.io.ValueSizeStrategy

org.jcvi.jillion.internal.core.residue

org.jcvi.jillion.internal.core.residue.org.jcvi.jillion.internal.core.residue.AbstractResidueSequence

org.jcvi.jillion.internal.core.seq.trace.sanger.chromat.ztr.data

org.jcvi.jillion.internal.core.seq.trace.sanger.chromat.ztr.data.org.jcvi.jillion.internal.core.seq.trace.sanger.chromat.ztr.data.Data

org.jcvi.jillion.internal.core.util

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.AbstractFOQueue

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.ArrayUtil

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.BoundedPriorityQueue

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.Caches

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.ComparableComparator

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.FIFOQueue

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableBitArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableByteArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableCharArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableIntArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableLongArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.GrowableShortArray

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.JillionUtil

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.LIFOQueue

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.RunLength

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.Sneak

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.ValidationException

org.jcvi.jillion.internal.core.util.org.jcvi.jillion.internal.core.util.Validator

org.jcvi.jillion.internal.core.util.iter

org.jcvi.jillion.internal.core.util.iter.org.jcvi.jillion.internal.core.util.iter.AbstractBlockingStreamingIterator

org.jcvi.jillion.internal.core.util.iter.org.jcvi.jillion.internal.core.util.iter.MergedSortedRecordIterator

org.jcvi.jillion.internal.core.util.iter.org.jcvi.jillion.internal.core.util.iter.PrimitiveArrayIterators

org.jcvi.jillion.internal.core.util.iter.org.jcvi.jillion.internal.core.util.iter.PushBackIterator

org.jcvi.jillion.internal.fasta

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.AbstractLargeFastaFileDataStore

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.AbstractResuseableFastaRecordVisitor

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.AdaptedFastaDataStore

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.DefaultFastaIndex

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.FastaIndex

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.FastaIndexRecord

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.FastaUtil

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.InMemorySortedFastaWriter

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.LargeFastaIdIterator

org.jcvi.jillion.internal.fasta.org.jcvi.jillion.internal.fasta.TmpDirSortedFastaWriter

org.jcvi.jillion.internal.fasta.aa

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.CommentedProteinFastaRecord

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.DefaultProteinFastaDataStore

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.IndexedProteinFastaFileDataStore

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.LargeProteinFastaFileDataStore

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.LargeProteinFastaIterator

org.jcvi.jillion.internal.fasta.aa.org.jcvi.jillion.internal.fasta.aa.UnCommentedProteinFastaRecord

org.jcvi.jillion.internal.fasta.nt

org.jcvi.jillion.internal.fasta.nt.org.jcvi.jillion.internal.fasta.nt.AdaptedNucleotideFastaDataStore

org.jcvi.jillion.internal.fasta.qual

org.jcvi.jillion.internal.fasta.qual.org.jcvi.jillion.internal.fasta.qual.DefaultQualityFastaFileDataStoreBuilder

org.jcvi.jillion.internal.fasta.qual.org.jcvi.jillion.internal.fasta.qual.IndexedQualityFastaFileDataStore

org.jcvi.jillion.internal.fasta.qual.org.jcvi.jillion.internal.fasta.qual.LargeQualityFastaFileDataStore

org.jcvi.jillion.internal.fasta.qual.org.jcvi.jillion.internal.fasta.qual.QualitySequenceFastaDataStoreIteratorImpl

org.jcvi.jillion.internal

org.jcvi.jillion.internal.org.jcvi.jillion.internal.package-info

org.jcvi.jillion.internal.sam

org.jcvi.jillion.internal.sam.org.jcvi.jillion.internal.sam.IndexerCallback

org.jcvi.jillion.internal.sam.org.jcvi.jillion.internal.sam.SamUtil

org.jcvi.jillion.internal.sam.index

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.BaiBin

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.BaiRefIndex

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.BamIndexer

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.BinBuilder

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.IndexUtil

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.ReferenceIndexBuilder

org.jcvi.jillion.internal.sam.index.org.jcvi.jillion.internal.sam.index.package-info

org.jcvi.jillion.internal.sam

org.jcvi.jillion.internal.sam.org.jcvi.jillion.internal.sam.package-info

org.jcvi.jillion.internal.trace.chromat

org.jcvi.jillion.internal.trace.chromat.org.jcvi.jillion.internal.trace.chromat.BasicChromatogram

org.jcvi.jillion.internal.trace.chromat.org.jcvi.jillion.internal.trace.chromat.BasicChromatogramBuilder

org.jcvi.jillion.internal.trace.chromat.org.jcvi.jillion.internal.trace.chromat.ChromatogramUtil

org.jcvi.jillion.internal.trace.chromat.org.jcvi.jillion.internal.trace.chromat.DefaultChannel

org.jcvi.jillion.internal.trace.chromat.org.jcvi.jillion.internal.trace.chromat.DefaultChannelGroup

org.jcvi.jillion.internal.trace.chromat.abi

org.jcvi.jillion.internal.trace.chromat.abi.org.jcvi.jillion.internal.trace.chromat.abi.AbiUtil

org.jcvi.jillion.internal.trace.chromat.abi.tag

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.AbstractTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultAsciiTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultDateTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultFloatTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultIntegerArrayTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultPascalStringTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultShortArrayTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultTimeTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultUserDefinedTaggedDataRecord

org.jcvi.jillion.internal.trace.chromat.abi.tag.org.jcvi.jillion.internal.trace.chromat.abi.tag.TaggedDataRecordBuilder

org.jcvi.jillion.internal.trace.chromat.abi.tag.rate

org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.DefaultScanRate

org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.DefaultScanRateTaggedDataType

org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.ScanRateUtils

org.jcvi.jillion.internal.trace.chromat.scf

org.jcvi.jillion.internal.trace.chromat.scf.org.jcvi.jillion.internal.trace.chromat.scf.PrivateDataImpl

org.jcvi.jillion.internal.trace.chromat.scf.org.jcvi.jillion.internal.trace.chromat.scf.SCFCodec

org.jcvi.jillion.internal.trace.chromat.scf.org.jcvi.jillion.internal.trace.chromat.scf.SCFCodecs

org.jcvi.jillion.internal.trace.chromat.scf.org.jcvi.jillion.internal.trace.chromat.scf.SCFUtils

org.jcvi.jillion.internal.trace.chromat.scf.org.jcvi.jillion.internal.trace.chromat.scf.ScfChromatogramImpl

org.jcvi.jillion.internal.trace.chromat.scf.header

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.DefaultSCFHeader

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.DefaultSCFHeaderCodec

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeader

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderCodec

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderDecoder

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderDecoderException

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderEncoder

org.jcvi.jillion.internal.trace.chromat.scf.header.org.jcvi.jillion.internal.trace.chromat.scf.header.package-info

org.jcvi.jillion.internal.trace.chromat.scf.header.pos

org.jcvi.jillion.internal.trace.chromat.scf.header.pos.org.jcvi.jillion.internal.trace.chromat.scf.header.pos.BytePositionStrategy

org.jcvi.jillion.internal.trace.chromat.scf.header.pos.org.jcvi.jillion.internal.trace.chromat.scf.header.pos.PositionStrategy

org.jcvi.jillion.internal.trace.chromat.scf.header.pos.org.jcvi.jillion.internal.trace.chromat.scf.header.pos.PositionStrategyFactory

org.jcvi.jillion.internal.trace.chromat.scf.header.pos.org.jcvi.jillion.internal.trace.chromat.scf.header.pos.ShortPositionStrategy

org.jcvi.jillion.internal.trace.chromat.scf.header.pos.org.jcvi.jillion.internal.trace.chromat.scf.header.pos.package-info

org.jcvi.jillion.internal.trace.chromat.scf.section

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.AbstractBasesSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.AbstractSampleSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.CommentSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.DefaultSectionCodecFactory

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.EncodedSection

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.NullSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.PrivateDataCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.Section

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.SectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.SectionCodecFactory

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.SectionDecoder

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.SectionDecoderException

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.SectionEncoder

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.Version2BasesSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.Version2SampleSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.Version3BasesSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.Version3SampleSectionCodec

org.jcvi.jillion.internal.trace.chromat.scf.section.org.jcvi.jillion.internal.trace.chromat.scf.section.package-info

org.jcvi.jillion.internal.trace.chromat.ztr

org.jcvi.jillion.internal.trace.chromat.ztr.org.jcvi.jillion.internal.trace.chromat.ztr.DefaultZTRChromatogramWriterBuilder

org.jcvi.jillion.internal.trace.chromat.ztr.org.jcvi.jillion.internal.trace.chromat.ztr.IOLibLikeZtrChromatogramWriter

org.jcvi.jillion.internal.trace.chromat.ztr.org.jcvi.jillion.internal.trace.chromat.ztr.ZTRChromatogramImpl

org.jcvi.jillion.internal.trace.chromat.ztr.org.jcvi.jillion.internal.trace.chromat.ztr.ZTRUtil

org.jcvi.jillion.internal.trace.chromat.ztr.org.jcvi.jillion.internal.trace.chromat.ztr.ZtrChromatogramWriter

org.jcvi.jillion.internal.trace.chromat.ztr.chunk

org.jcvi.jillion.internal.trace.chromat.ztr.chunk.org.jcvi.jillion.internal.trace.chromat.ztr.chunk.Chunk

org.jcvi.jillion.internal.trace.chromat.ztr.chunk.org.jcvi.jillion.internal.trace.chromat.ztr.chunk.ChunkException

org.jcvi.jillion.internal.trace.chromat.ztr.chunk.org.jcvi.jillion.internal.trace.chromat.ztr.chunk.ChunkType

org.jcvi.jillion.internal.trace.chromat.ztr.chunk.org.jcvi.jillion.internal.trace.chromat.ztr.chunk.package-info

org.jcvi.jillion.internal.trace.chromat.ztr.data

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.DataFactory

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.DataHeader

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.DeltaEncodedData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.DeltaStrategy

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.FollowData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.RawData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.RunLengthEncodedData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.ShrinkToEightBitData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.ZLibData

org.jcvi.jillion.internal.trace.chromat.ztr.data.org.jcvi.jillion.internal.trace.chromat.ztr.data.package-info

org.jcvi.jillion.internal.trace.fastq

org.jcvi.jillion.internal.trace.fastq.org.jcvi.jillion.internal.trace.fastq.CommentedParsedFastqRecord

org.jcvi.jillion.internal.trace.fastq.org.jcvi.jillion.internal.trace.fastq.ParsedFastqRecord

org.jcvi.jillion.internal.trace.fastq.org.jcvi.jillion.internal.trace.fastq.ParsedQualitySequence

org.jcvi.jillion.maq.bfa

org.jcvi.jillion.maq.bfa.org.jcvi.jillion.maq.bfa.BfaParser

org.jcvi.jillion.maq.bfa.org.jcvi.jillion.maq.bfa.BfaWriterBuilder

org.jcvi.jillion.maq.bfa.org.jcvi.jillion.maq.bfa.package-info

org.jcvi.jillion.maq.bfq

org.jcvi.jillion.maq.bfq.org.jcvi.jillion.maq.bfq.BfqFileDataStoreBuilder

org.jcvi.jillion.maq.bfq.org.jcvi.jillion.maq.bfq.BfqFileParser

org.jcvi.jillion.maq.bfq.org.jcvi.jillion.maq.bfq.BfqFileWriterBuilder

org.jcvi.jillion.maq.bfq.org.jcvi.jillion.maq.bfq.package-info

org.jcvi.jillion.maq

org.jcvi.jillion.maq.org.jcvi.jillion.maq.package-info

org.jcvi.jillion.orf

org.jcvi.jillion.orf.org.jcvi.jillion.orf.Orf

org.jcvi.jillion.orf.org.jcvi.jillion.orf.OrfFinder

org.jcvi.jillion.profile

org.jcvi.jillion.profile.org.jcvi.jillion.profile.BaseCount

org.jcvi.jillion.profile.org.jcvi.jillion.profile.DisplayCountStrategy

org.jcvi.jillion.profile.org.jcvi.jillion.profile.MostFrequentTieBreakerRule

org.jcvi.jillion.profile.org.jcvi.jillion.profile.ProfileWriter

org.jcvi.jillion.profile.org.jcvi.jillion.profile.ProfileWriterBuilder

org.jcvi.jillion.profile.org.jcvi.jillion.profile.SimpleProfileWriter

org.jcvi.jillion.profile.org.jcvi.jillion.profile.package-info

org.jcvi.jillion.sam

org.jcvi.jillion.sam.org.jcvi.jillion.sam.AbstractSamFileParser

org.jcvi.jillion.sam.org.jcvi.jillion.sam.AbstractSamVisitor

org.jcvi.jillion.sam.org.jcvi.jillion.sam.BamFileParser

org.jcvi.jillion.sam.org.jcvi.jillion.sam.BgzfInputStream

org.jcvi.jillion.sam.org.jcvi.jillion.sam.BgzfOutputStream

org.jcvi.jillion.sam.org.jcvi.jillion.sam.DefaultSamFileDataStore

org.jcvi.jillion.sam.org.jcvi.jillion.sam.Encoding

org.jcvi.jillion.sam.org.jcvi.jillion.sam.IndexedBamFileParser

org.jcvi.jillion.sam.org.jcvi.jillion.sam.NullSamAttributeValidator

org.jcvi.jillion.sam.org.jcvi.jillion.sam.PresortedBamFileWriter

org.jcvi.jillion.sam.org.jcvi.jillion.sam.PresortedSamFileWriter

org.jcvi.jillion.sam.org.jcvi.jillion.sam.QuerySortedSamFileDataStore

org.jcvi.jillion.sam.org.jcvi.jillion.sam.ReSortSamFileWriter

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamAttributed

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamFileDataStore

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamFileDataStoreBuilder

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamFileParser

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamFileWriterBuilder

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamParser

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamParserFactory

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamRecord

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamRecordBuilder

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamRecordFlag

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamRecordFlags

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamRecordImpl

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamValidationException

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamVisitor

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SamWriter

org.jcvi.jillion.sam.org.jcvi.jillion.sam.SortOrder

org.jcvi.jillion.sam.org.jcvi.jillion.sam.VirtualFileOffset

org.jcvi.jillion.sam.attribute

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.ChainedSamAttributeValidatorBuilder

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.InvalidAttributeException

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.InvalidValueTypeException

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.NoDuplicateAttributeValidator

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.ReservedAttributeValidator

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.ReservedSamAttributeKeys

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.SamAttribute

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.SamAttributeKey

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.SamAttributeKeyFactory

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.SamAttributeType

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.SamAttributeValidator

org.jcvi.jillion.sam.attribute.org.jcvi.jillion.sam.attribute.package-info

org.jcvi.jillion.sam.cigar

org.jcvi.jillion.sam.cigar.org.jcvi.jillion.sam.cigar.Cigar

org.jcvi.jillion.sam.cigar.org.jcvi.jillion.sam.cigar.CigarElement

org.jcvi.jillion.sam.cigar.org.jcvi.jillion.sam.cigar.CigarOperation

org.jcvi.jillion.sam.cigar.org.jcvi.jillion.sam.cigar.package-info

org.jcvi.jillion.sam.header

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamHeader

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamHeaderBuilder

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamHeaderTag

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamHeaderTagKey

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamProgram

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamProgramBuilder

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamReadGroup

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamReadGroupBuilder

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamReferenceSequence

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamReferenceSequenceBuilder

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.SamVersion

org.jcvi.jillion.sam.header.org.jcvi.jillion.sam.header.package-info

org.jcvi.jillion.sam.index

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.BamIndex

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.BamIndexFileWriterBuilder

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.Bin

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.Chunk

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.ReferenceIndex

org.jcvi.jillion.sam.index.org.jcvi.jillion.sam.index.package-info

org.jcvi.jillion.sam

org.jcvi.jillion.sam.org.jcvi.jillion.sam.package-info

org.jcvi.jillion.sam.transform

org.jcvi.jillion.sam.transform.org.jcvi.jillion.sam.transform.PaddedSamTransformationService

org.jcvi.jillion.sam.transform.org.jcvi.jillion.sam.transform.SamGappedReferenceBuilderVisitor

org.jcvi.jillion.sam.transform.org.jcvi.jillion.sam.transform.SamTransformationService

org.jcvi.jillion.sam.transform.org.jcvi.jillion.sam.transform.package-info

org.jcvi.jillion.shared.fasta

org.jcvi.jillion.shared.fasta.org.jcvi.jillion.shared.fasta.AbstractFastaFileDataStoreBuilder

org.jcvi.jillion.shared.fasta.org.jcvi.jillion.shared.fasta.AbstractFastaRecordBuilder

org.jcvi.jillion.shared.fasta.org.jcvi.jillion.shared.fasta.AbstractFastaRecordWriter

org.jcvi.jillion.shared.fasta.org.jcvi.jillion.shared.fasta.AbstractResidueFastaWriter

org.jcvi.jillion.shared.fasta.org.jcvi.jillion.shared.fasta.package-info

org.jcvi.jillion.shared

org.jcvi.jillion.shared.org.jcvi.jillion.shared.package-info

org.jcvi.jillion.testutils

org.jcvi.jillion.testutils.org.jcvi.jillion.testutils.NucleotideSequenceTestUtil

org.jcvi.jillion.testutils.org.jcvi.jillion.testutils.ProteinSequenceTestUtil

org.jcvi.jillion.testutils.assembly.cas

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.CasParserTestDouble

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.CasTestUtil

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.DefaultCasAlignment

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.DefaultCasAlignmentRegion

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.FastaRecordWriter

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.FastqRecordWriter

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.RecordWriter

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.SffRecordWriter

org.jcvi.jillion.testutils.assembly.cas.org.jcvi.jillion.testutils.assembly.cas.package-info

org.jcvi.jillion.trace

org.jcvi.jillion.trace.org.jcvi.jillion.trace.Trace

org.jcvi.jillion.trace.org.jcvi.jillion.trace.TraceDataStore

org.jcvi.jillion.trace.org.jcvi.jillion.trace.TraceNucleotideDataStoreAdapter

org.jcvi.jillion.trace.org.jcvi.jillion.trace.TraceQualityDataStoreAdapter

org.jcvi.jillion.trace.chromat

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.Channel

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.ChannelGroup

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.Chromatogram

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.ChromatogramFactory

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.ChromatogramFileVisitor

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.ChromatogramWriter

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.EncodedShortData

org.jcvi.jillion.trace.chromat.abi

org.jcvi.jillion.trace.chromat.abi.org.jcvi.jillion.trace.chromat.abi.AbiChromatogram

org.jcvi.jillion.trace.chromat.abi.org.jcvi.jillion.trace.chromat.abi.AbiChromatogramBuilder

org.jcvi.jillion.trace.chromat.abi.org.jcvi.jillion.trace.chromat.abi.AbiChromatogramFileVisitor

org.jcvi.jillion.trace.chromat.abi.org.jcvi.jillion.trace.chromat.abi.AbiChromatogramParser

org.jcvi.jillion.trace.chromat.abi.org.jcvi.jillion.trace.chromat.abi.package-info

org.jcvi.jillion.trace.chromat.abi.tag

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.Ab1LocalDate

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.Ab1LocalTime

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.AsciiTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.ByteArrayTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.DateTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.FloatArrayTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.IntArrayTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.PascalStringTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.ShortArrayTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.StringTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataName

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataType

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.TimeTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.org.jcvi.jillion.trace.chromat.abi.tag.UserDefinedTaggedDataRecord

org.jcvi.jillion.trace.chromat.abi.tag.rate

org.jcvi.jillion.trace.chromat.abi.tag.rate.org.jcvi.jillion.trace.chromat.abi.tag.rate.ScanRate

org.jcvi.jillion.trace.chromat.abi.tag.rate.org.jcvi.jillion.trace.chromat.abi.tag.rate.ScanRateTaggedDataType

org.jcvi.jillion.trace.chromat

org.jcvi.jillion.trace.chromat.org.jcvi.jillion.trace.chromat.package-info

org.jcvi.jillion.trace.chromat.scf

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.PrivateData

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfChromatogram

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfChromatogramBuilder

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfChromatogramFileVisitor

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfChromatogramParser

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfChromatogramWriterBuilder

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.ScfDecoderException

org.jcvi.jillion.trace.chromat.scf.org.jcvi.jillion.trace.chromat.scf.package-info

org.jcvi.jillion.trace.chromat.ztr

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogram

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramBuilder

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramFileVisitor

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramParser

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramWriterBuilder

org.jcvi.jillion.trace.chromat.ztr.org.jcvi.jillion.trace.chromat.ztr.package-info

org.jcvi.jillion.trace.fastq

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.AbstractFastqRecordVisitor

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.AbstractFastqVisitor

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.CommentedFastqRecord

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.DefaultFastqFileDataStore

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqCollectors

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqDataStore

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileDataStore

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileDataStoreBuilder

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileDataStoreImpl

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileParser

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileParserBuilder

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqFileReader

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqParser

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqQualityCodec

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqRecord

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqRecordBuilder

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqRecordBuilderImpl

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqRecordVisitor

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqUtil

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqVisitor

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqWriter

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqWriterAdapter

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.FastqWriterBuilder

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.IlluminaUtil

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.InMemorySortedFastqWriter

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.IndexedFastqFileDataStore

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.LargeFastqFileDataStore

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.SolexaUtil

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.SplitFastqWriter

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.TmpDirSortedFastqWriter

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.UncommentedFastqRecord

org.jcvi.jillion.trace.fastq.org.jcvi.jillion.trace.fastq.package-info

org.jcvi.jillion.trace.sff

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.CompletelyParsedIndexedSffFileDataStore

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSFFCommonHeaderDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffCommonHeader

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffFileDataStore

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffReadData

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffReadDataDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffReadHeader

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.DefaultSffReadHeaderDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.LargeSffFileDataStore

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.ManifestIndexed454SffFileDataStore

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.Sff454NameUtil

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffCommonHeader

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffCommonHeaderDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffDataStoreBuilder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffDecoderException

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFileDataStore

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFileDataStoreBuilder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFileIterator

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFileParser

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFileReadVisitor

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFlowgram

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffFlowgramImpl

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffParser

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffReadData

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffReadDataDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffReadHeader

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffReadHeaderDecoder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffUtil

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffVisitor

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffVisitorCallback

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffWriter

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffWriterBuilder

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.SffWriterUtil

org.jcvi.jillion.trace.sff.org.jcvi.jillion.trace.sff.package-info

org.jcvi.jillion.trim

org.jcvi.jillion.trim.org.jcvi.jillion.trim.BwaQualityTrimmer

org.jcvi.jillion.trim.org.jcvi.jillion.trim.NucleotideTrimmer

org.jcvi.jillion.trim.org.jcvi.jillion.trim.QualityTrimmer

org.jcvi.jillion.trim.org.jcvi.jillion.trim.Trimmer

org.jcvi.jillion.trim.org.jcvi.jillion.trim.TrimmerPipeline

org.jcvi.jillion.trim.org.jcvi.jillion.trim.TrimmerPipelineBuilder

org.jcvi.jillion.trim.lucy

org.jcvi.jillion.trim.lucy.org.jcvi.jillion.trim.lucy.LucyQualityTrimmerBuilder

org.jcvi.jillion.trim.lucy.org.jcvi.jillion.trim.lucy.LucyVectorSpliceTrimmerBuilder

org.jcvi.jillion.trim.lucy.org.jcvi.jillion.trim.lucy.lucy.matrix

org.jcvi.jillion.trim.lucy.org.jcvi.jillion.trim.lucy.package-info

org.jcvi.jillion.trim.trimmomatic

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.AbstractEdgeQualityTrimmer

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.LeadingQualityTrimmer

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.MaxInfoTrimmer

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.SlidingWindowQualityTrimmer

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.TrailingQualityTrimmer

org.jcvi.jillion.trim.trimmomatic.org.jcvi.jillion.trim.trimmomatic.package-info

org.jcvi

org.jcvi.org.jcvi.package-info

.overview-summary.html