A B C D E F G H I J K L M N O P R S T U V W X

A

AbstractDBAnnotationDriver<RecordType> - Class in de.charite.compbio.jannovar.vardbs.base

Abstract base class for annotation based on VCF files.

AbstractDBAnnotationDriver(String, String, DBAnnotationOptions, VariantContextToRecordConverter<RecordType>) - Constructor for class de.charite.compbio.jannovar.vardbs.base.AbstractDBAnnotationDriver

Create annotation driver for a coordinate-sorted, bgzip-compressed, VCF file

AbstractMendelianChecker - Class in de.charite.compbio.jannovar.mendel.impl

Abstract base class for mendelian checkers

AbstractMendelianChecker(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker

AbstractVariantContextCompatibilityChecker - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker

Abstract helper class for checking a List of VariantContext for compatibility with a Pedigree .

AbstractVariantContextCompatibilityChecker(Pedigree, List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

Initialize compatibility checker and perform some sanity checks.

AbstractVariantContextCompatibilityChecker(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

Initialize compatibility checker and perform some sanity checks.

AD - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

Constant for autosomal dominant

add(NucleotideChange) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

add(int, NucleotideChange) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

add(ProteinChange) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

add(int, ProteinChange) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

addAll(Collection<? extends NucleotideChange>) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

addAll(int, Collection<? extends NucleotideChange>) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

addAll(Collection<? extends ProteinChange>) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

addAll(int, Collection<? extends ProteinChange>) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

addCompatibleMode(ModeOfInheritance) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

addExonRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

addGenotypes(ImmutableList<Genotype>) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

Adds new list of genotypes, one for each individual.

addHeaders(VCFHeader, String) - Method in class de.charite.compbio.jannovar.vardbs.base.VCFHeaderExtender

Add header entries with a given prefix.

addHeaders(VCFHeader) - Method in class de.charite.compbio.jannovar.vardbs.base.VCFHeaderExtender

Add headers with default prefix

addHeaders(VCFHeader, String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVCFHeaderExtender

addHeaders(VCFHeader, String) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacVCFHeaderExtender

addHeaders(VCFHeader, String) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KVCFHeaderExtender

addHeadersInfixes(VCFHeader, String, String, String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVCFHeaderExtender

addHeadersInfixes(VCFHeader, String, String, String) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KVCFHeaderExtender

addMatchInheritance(ModeOfInheritance) - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext

Add a mode of inheritance to this variant.

addMode(ModeOfInheritance) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder

Add a ModeOfInheritance to the builder.

addModes(Collection<ModeOfInheritance>) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder

Add a collection of ModeOfInheritance to the builder.

AllAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation

Deprecated.

AllAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.AllAnnotationListTextGenerator

Deprecated.

AlleleMatcher - Class in de.charite.compbio.jannovar.vardbs.base

Find matches between two allels (an observed and a database variant) This class is an implementation detail and not part of the public interface.

AlleleMatcher(String) - Constructor for class de.charite.compbio.jannovar.vardbs.base.AlleleMatcher

Construct GenotypeMatcher

allLeftOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

AminoAcidChange - Class in de.charite.compbio.jannovar.reference

Representation of a change in amino acids.

AminoAcidChange(int, String, String) - Constructor for class de.charite.compbio.jannovar.reference.AminoAcidChange

Construct object with given values.

AminoAcidChangeNormalizer - Class in de.charite.compbio.jannovar.reference

Helper for normalizing changes in amino acid sequences.

AminoAcidChangeNormalizer() - Constructor for class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

AminoAcidCode - Enum in de.charite.compbio.jannovar.hgvs

Representation of the two possible amino acid codes, 1-letter and 3-letter.

AnnotatedVariantWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf

Interface for output writers in Jannovar class.

AnnotatedVariantWriter() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter

AnnotatedVCFWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf

Annotate variant in VariantContext and write out through HTSJDK (i.e.

AnnotatedVCFWriter(ReferenceDictionary, VCFHeader, ImmutableMap<Integer, Chromosome>, String, JannovarOptions, ImmutableList<String>) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter

AnnotatePositionCommand - Class in de.charite.compbio.jannovar.cmd.annotate_pos

Allows the annotation of a single position.

AnnotatePositionCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand

AnnotatePositionCommandLineParser - Class in de.charite.compbio.jannovar.cmd.annotate_pos

Parse the command line for the "annotate-position" command.

AnnotatePositionCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser

annotateRecord(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator

Annotate VariantContext with compatibility for Mendelian inheritance

annotateRecords(List<VariantContext>) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator

Annotate List of VariantContext objects

annotateVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.vardbs.base.AbstractDBAnnotationDriver

annotateVariantContext(VariantContext) - Method in interface de.charite.compbio.jannovar.vardbs.base.DBAnnotationDriver

Annotate the VariantContext object using the information in the database.

annotateVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator

Annotate one VariantContext with information from a database

annotateVariantContexts(Collection<VariantContext>) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator

Convenience method for bulk-annotating multiple VariantContext objects

AnnotateVCFCommand - Class in de.charite.compbio.jannovar.cmd.annotate_vcf

Run annotation steps (read in VCF, write out VCF or Jannovar file format).

AnnotateVCFCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand

AnnotateVCFCommandLineParser - Class in de.charite.compbio.jannovar.cmd.annotate_vcf

Parser for annotate-vcf command line.

AnnotateVCFCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser

AnnotatingRecord<RecordType> - Class in de.charite.compbio.jannovar.vardbs.base

Helper for packing allele number together with RecordType.

AnnotatingRecord(RecordType, int) - Constructor for class de.charite.compbio.jannovar.vardbs.base.AnnotatingRecord

Annotation - Class in de.charite.compbio.jannovar.annotation

Collect the information for one variant's annotation.

Annotation(Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize object with messages only.

Annotation(TranscriptModel, GenomeVariant, Collection<VariantEffect>, AnnotationLocation, NucleotideChange, NucleotideChange, ProteinChange) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize the Annotation with the given values.

Annotation(TranscriptModel, GenomeVariant, Collection<VariantEffect>, AnnotationLocation, NucleotideChange, NucleotideChange, ProteinChange, Collection<AnnotationMessage>) - Constructor for class de.charite.compbio.jannovar.annotation.Annotation

Initialize the Annotation with the given values.

AnnotationBuilderDispatcher - Class in de.charite.compbio.jannovar.annotation.builders

Dispatches annotation building to the specific classes, depending on their GenomeVariant.getType().

AnnotationBuilderDispatcher(TranscriptModel, GenomeVariant, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher

AnnotationBuilderOptions - Class in de.charite.compbio.jannovar.annotation.builders

Configuration for the AnnotationBuilder subclasses.

AnnotationBuilderOptions() - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

AnnotationBuilderOptions(boolean) - Constructor for class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

AnnotationException - Exception in de.charite.compbio.jannovar.annotation

Annotation exceptions are thrown when the information provided is not well formed or not sufficient to create a correct annotation.

AnnotationException() - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationException(String) - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.annotation.AnnotationException

AnnotationLocation - Class in de.charite.compbio.jannovar.annotation

Describes the location of an annotation.

AnnotationLocation(TranscriptModel, AnnotationLocation.RankType, int, int, TranscriptInterval) - Constructor for class de.charite.compbio.jannovar.annotation.AnnotationLocation

AnnotationLocation.RankType - Enum in de.charite.compbio.jannovar.annotation

Enumeration for rank types, exon, intron, or neither (i.e.

AnnotationLocationBuilder - Class in de.charite.compbio.jannovar.annotation

Builder for the immutable AnnotationLocation class.

AnnotationLocationBuilder() - Constructor for class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationMessage - Enum in de.charite.compbio.jannovar.annotation

Error messages for encoding problems during the annotation.

AnnotationTextGenerator - Class in de.charite.compbio.jannovar.annotation

Deprecated.

applyAnnotations(VariantContext, List<VariantAnnotations>) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Write annotations from annos to vc

AR - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

Constant for autosomal recessive

B

BestAnnotationListTextGenerator - Class in de.charite.compbio.jannovar.annotation

Deprecated.

BestAnnotationListTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.BestAnnotationListTextGenerator

Deprecated.

BlockSubstitutionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the block substitution GenomeVariant in the given TranscriptModel .

BlockSubstitutionAnnotationBuilder(TranscriptModel, GenomeVariant, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher

build() - Method in class de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.DeletionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.InsertionAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder

build() - Method in class de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder

Build annotation for StructuralVariantAnnotationBuilder.transcript and StructuralVariantAnnotationBuilder.change

build() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

build(String, boolean) - Method in class de.charite.compbio.jannovar.datasource.JannovarDataFactory

build(boolean, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

build(boolean, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

build(boolean, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

build(boolean, NucleotideMiscChangeType) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

Static factory function that forwards to NucleotideMiscChange.NucleotideMiscChange(boolean, NucleotideMiscChangeType).

build(boolean, NucleotideRange, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

Factory forwards to NucleotideShortSequenceRepeatVariability.NucleotideShortSequenceRepeatVariability(boolean, NucleotideRange, int, int).

build(boolean, int, String, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

Build NucleotideSubstitution with nucleotide positions without offset values.

build(int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

build(int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

build(SequenceType, String, NucleotideChangeAllele...) - Static method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

build(VariantConfiguration, NucleotideChange...) - Static method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

build(SequenceType, String, VariantConfiguration, NucleotideChange...) - Static method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

build(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

Construct normal ProteinExtension

build(boolean, ProteinPointLocation, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

Construct normal ProteinExtension

build(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift with full settings

build(boolean, ProteinPointLocation, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift with full settings

build(boolean, ProteinMiscChangeType) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

Static factory function that forwards to ProteinMiscChange.ProteinMiscChange(boolean, ProteinMiscChangeType).

build(boolean, String, int, String, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

Factory forwards to ProteinShortSequenceRepeatVariability.build(boolean, ProteinRange, int, int)

build(boolean, ProteinRange, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

Factory forwards to ProteinShortSequenceRepeatVariability.ProteinShortSequenceRepeatVariability(boolean, ProteinRange, int, int)

build(boolean, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

Factory method for direct construction from source AA, position, and targetAA.

build(String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

build(String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

build(String, ProteinChangeAllele...) - Static method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

build(VariantConfiguration, ProteinChange...) - Static method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

build(String, VariantConfiguration, ProteinChange...) - Static method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

build(boolean, boolean) - Static method in enum de.charite.compbio.jannovar.htsjdk.InfoFields

build() - Method in class de.charite.compbio.jannovar.mendel.GenotypeBuilder

build() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

build() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder

Build the InheritanceCompatibilityChecker.

build() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

build() - Static method in class de.charite.compbio.jannovar.reference.HG19RefDictBuilder

build() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

build(VCFHeader) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfoFactory

build() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

build() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

build() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

buildAnnotations(int, int, String, String, PositionType) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotator

Convenience function for obtaining an VariantAnnotations from genome change in primitive types.

buildAnnotations(GenomeVariant) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotator

Main entry point to getting Annovar-type annotations for a variant identified by chromosomal coordinates.

buildAnnotations(VariantContext) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Given a VariantContext, generate one VariantAnnotations for each alternative allele.

buildDownstreamOfCDS(int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

buildDownstreamOfTerminal(boolean, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

buildDownstreamOfTerminal(String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

buildDownstreamOfTerminal(String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

buildEffectText() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

buildEmptyList(GenomeVariant) - Static method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

Builder() - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder

default constructor.

buildErrorAnnotations(GenomeVariant) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

buildExonicLocation(int, int) - Static method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

Construct LegacyLocationType.EXONIC location

buildFromString(String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

Build from input string.

buildGenomeVariant(VariantContext, int) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Build a GenomeVariant from a VariantContext object.

buildHGVSText(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

buildIntronicLocation(int, int) - Static method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

Construct LegacyLocationType.INTRONIC location

buildShort(boolean, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift short description

buildShort(boolean, ProteinPointLocation) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift short description

buildSiblings() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

buildWithLength(boolean, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithLength(boolean, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithLength(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build without offset and with length information

buildWithLength(boolean, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build without offset and no sequence description

buildWithLength(boolean, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build without offset and with length information

buildWithLength(boolean, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithLength(boolean, String, int, String, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion with length information

buildWithLength(boolean, String, int, String, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

buildWithLength(boolean, String, int, String, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

Build with length information

buildWithLength(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

Build without any sequence description.

buildWithLength(boolean, String, int, String, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

Build with length information

buildWithOffset(boolean, int, int, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithOffset(boolean, int, int, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithOffset(boolean, int, int, int, int, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithOffset(boolean, int, int, String, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

Build NucleotideSubstitution with nucleotide positions with offset values.

buildWithOffset(int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

buildWithOffset(boolean, String, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

buildWithOffset(String, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

buildWithOffset(String, int, int, String, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

buildWithOffsetWithLength(boolean, int, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithOffsetWithLength(boolean, int, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithOffsetWithLength(boolean, int, int, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build with length information

buildWithOffsetWithLength(boolean, int, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build with length information

buildWithOffsetWithLength(boolean, int, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithOffsetWithoutSeqDescription(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithOffsetWithoutSeqDescription(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithOffsetWithoutSeqDescription(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build without any sequence description

buildWithOffsetWithoutSeqDescription(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build without any sequence description

buildWithOffsetWithoutSeqDescription(boolean, int, int, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithOffsetWithSeqDescription(boolean, int, int, int, int, NucleotideSeqDescription, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build with sequence description

buildWithOffsetWithSequence(boolean, int, int, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithOffsetWithSequence(boolean, int, int, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithOffsetWithSequence(boolean, int, int, int, int, String, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build with sequence information

buildWithOffsetWithSequence(boolean, int, int, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build with sequence

buildWithOffsetWithSequence(boolean, int, int, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithoutOffset(int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

buildWithoutSeqDescription(boolean, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithoutSeqDescription(boolean, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithoutSeqDescription(boolean, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build without offset and any sequence description

buildWithoutSeqDescription(boolean, int, int) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithoutSeqDescription(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion without length and sequence information

buildWithoutSeqDescription(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

buildWithoutSeqDescription(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

Build without any sequence description

buildWithoutSeqDescription(boolean, String, int, String, int) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

Build without any SeqDescription

buildWithoutTerminal(boolean, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

Construct ProteinExtension without a terminal in the extension

buildWithoutTerminal(boolean, ProteinPointLocation, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

Construct ProteinExtension without a terminal in the extension

buildWithoutTerminal(boolean, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift for the case that there is no terminal

buildWithoutTerminal(boolean, ProteinPointLocation, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Build new ProteinFrameshift for the case that there is no terminal

buildWithSeqDescription(boolean, int, int, NucleotideSeqDescription, NucleotideSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build without offset and with sequence description

buildWithSeqDescription(boolean, String, int, String, int, ProteinSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

buildWithSeqDescription(boolean, String, int, String, int, ProteinSeqDescription, ProteinSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

Build with sequence description

buildWithSeqDescription(boolean, String, int, String, int, ProteinSeqDescription) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

Build with SeqDescription

buildWithSequence(boolean, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

buildWithSequence(boolean, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

buildWithSequence(boolean, int, int, String, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

Build without offset and with sequence information

buildWithSequence(boolean, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

Build without offset and with sequence

buildWithSequence(boolean, int, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

buildWithSequence(boolean, String, int, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion with sequence

buildWithSequence(boolean, String, int, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

buildWithSequence(boolean, String, int, String, int, String, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

Build with sequence information

buildWithSequence(boolean, String, int, String, int, String) - Static method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

Build with sequence

C

CannotAnnotateMendelianInheritance - Exception in de.charite.compbio.jannovar.mendel.bridge

Raised in the case of problems with annotating Mendelian inheritance

CannotAnnotateMendelianInheritance(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance

CannotAnnotateMendelianInheritance(String) - Constructor for exception de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance

CannotTranslateHGVSVariant - Exception in de.charite.compbio.jannovar.hgvs.bridge

Helper class thrown on problems with translating HGVSVariant to GenomeVariant.

CannotTranslateHGVSVariant() - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant

CannotTranslateHGVSVariant(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant

CannotTranslateHGVSVariant(String) - Constructor for exception de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant

CDSInterval - Class in de.charite.compbio.jannovar.reference

Interval on a transcript.

CDSInterval(TranscriptModel, int, int) - Constructor for class de.charite.compbio.jannovar.reference.CDSInterval

construct transcript interval with one-based coordinate system

CDSInterval(TranscriptModel, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.CDSInterval

construct transcript interval with selected coordinate system

CDSPosition - Class in de.charite.compbio.jannovar.reference

Position on a transcript.

CDSPosition(TranscriptModel, int) - Constructor for class de.charite.compbio.jannovar.reference.CDSPosition

construct transcript position with one-based coordinate system

CDSPosition(TranscriptModel, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.CDSPosition

construct transcript position with selected coordinate system

cdsToGenomePos(CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from CDS to genome position.

cdsToTranscriptPos(CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from CDS to transcript position.

cdsTranscriptLength() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

check(List<VariantContext>) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

Method for checking whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.

checkMendelianInheritance(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

Perform checking for compatible mode of inheritance

chromosomalChanges - Variable in class de.charite.compbio.jannovar.JannovarOptions

chromosomal position and a change, e.g.

Chromosome - Class in de.charite.compbio.jannovar.data

This class encapsulates a chromosome and all of the genes its contains.

Chromosome(ReferenceDictionary, int, IntervalArray<TranscriptModel>) - Constructor for class de.charite.compbio.jannovar.data.Chromosome

Initialize object.

ChromosomeType - Enum in de.charite.compbio.jannovar.mendel

Describe the chromosome type, for use in mendelian inheritance filtering

clear() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

clear() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

clearAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Clear alternative geneIDs map

clearExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Clear exon regions list

close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter

Close writer, free resources

close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter

Close VariantContextWriter in out.

close() - Method in class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor

close() - Method in class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker

close() - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor

close() - Method in interface de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor

Mark processing as done, no more variants will come in.

codonWithUpdatedBase(String, int, char) - Static method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Update the base given by frameShift in the given codon string transcriptCodon to targetNC and return updated codon.

command - Variable in class de.charite.compbio.jannovar.JannovarOptions

the selected command

CommandLineParsingException - Exception in de.charite.compbio.jannovar.cmd

Exception thrown on problems with the command line.

CommandLineParsingException() - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException

CommandLineParsingException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException

CommandLineParsingException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.Annotation

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

compareTo(Interval<T>) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

compareTo(MutableInterval<T>) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

compareTo(FeatureRecord) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

compareTo(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

compareTo(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

compareTo(Annotation) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

compareTo(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

compareTo(Annotation) - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

computeCompatibleInheritanceModes(List<VariantContext>) - Method in class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator

Compute compatible modes of inheritance for a list of VariantContext objects

concatenate(Object...) - Static method in class de.charite.compbio.jannovar.impl.util.StringUtil

Concatenate values.toString() using a StringBuilder.

construct(SAMSequenceDictionary) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionListFactoryFromSAMSequenceDictionary

constructDBSNP(String, String, DBAnnotationOptions) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotatorFactory

Construct dbSNP VariantContext annotator factory.

constructExac(String, String, DBAnnotationOptions) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotatorFactory

Construct ExAC VariantContext annotator factory.

constructSingleSamplePedigree(String) - Static method in class de.charite.compbio.jannovar.pedigree.Pedigree

constructUK10K(String, String, DBAnnotationOptions) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotatorFactory

Construct UK10K VariantContext annotator factory.

constructVCFHeaderExtender() - Method in interface de.charite.compbio.jannovar.vardbs.base.DBAnnotationDriver

constructVCFHeaderExtender() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPAnnotationDriver

constructVCFHeaderExtender() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacAnnotationDriver

constructVCFHeaderExtender() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KAnnotationDriver

ConsumerProcessor - Class in de.charite.compbio.jannovar.mendel.filter

Call a function for each variant put into the pipeline step

ConsumerProcessor(Consumer<VariantContext>) - Constructor for class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor

contains(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

contains(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

contains(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

contains(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

contains(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

containsAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

containsAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

containsExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

convert(VariantContext) - Method in interface de.charite.compbio.jannovar.vardbs.base.VariantContextToRecordConverter

Convert VariantContext into record type T

ConvertibleToHGVSString - Interface in de.charite.compbio.jannovar.hgvs

Provide HGVS string representation of an element.

CoordinateSortingChecker - Class in de.charite.compbio.jannovar.mendel.filter

Check that the VCF file is sorted by coordinate Since VCF files do not have to provide a reference name dictionary in their header, validating the sort order of the chromosomes is tricky.

CoordinateSortingChecker(VariantContextProcessor) - Constructor for class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker

Initialize the checker

createDefaults() - Static method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

D

DatabaseListCommand - Class in de.charite.compbio.jannovar.cmd.db_list

DatabaseListCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand

DatabaseListCommandLineParser - Class in de.charite.compbio.jannovar.cmd.db_list

DatabaseListCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser

Calls initializeParser().

dataFile - Variable in class de.charite.compbio.jannovar.JannovarOptions

path to the file with the serialized data

DataSource - Class in de.charite.compbio.jannovar.datasource

Base class for all data sources.

DataSourceFactory - Class in de.charite.compbio.jannovar.datasource

Factory class that allows the construction of DataSource objects as configured in INI files.

DataSourceFactory(DatasourceOptions, ImmutableList<String>) - Constructor for class de.charite.compbio.jannovar.datasource.DataSourceFactory

dataSourceFiles - Variable in class de.charite.compbio.jannovar.JannovarOptions

paths to INI files ot use for parsing

dataSourceNames - Variable in class de.charite.compbio.jannovar.JannovarOptions

data source name to use for downloading and parsing

DatasourceOptions - Class in de.charite.compbio.jannovar.datasource

Configuration for data sources.

DatasourceOptions() - Constructor for class de.charite.compbio.jannovar.datasource.DatasourceOptions

Initialize with default settings.

DatasourceOptions(URL, URL, URL, boolean) - Constructor for class de.charite.compbio.jannovar.datasource.DatasourceOptions

DBAnnotationDriver - Interface in de.charite.compbio.jannovar.vardbs.base

Interface for annotation drivers by variant databases.

DBAnnotationOptions - Class in de.charite.compbio.jannovar.vardbs.base

Configuration for annotating variants with information from databases.

DBAnnotationOptions(boolean, boolean, String, DBAnnotationOptions.MultipleMatchBehaviour) - Constructor for class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

DBAnnotationOptions.MultipleMatchBehaviour - Enum in de.charite.compbio.jannovar.vardbs.base

Enum for representing behaviour in the case of multiple matches

DBSNPAnnotationDriver - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Annotation driver class for annotations using dbSNP

DBSNPAnnotationDriver(String, String, DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPAnnotationDriver

Create annotation driver for a coordinate-sorted, bgzip-compressed, dbSNP VCF file

DBSNPGeneInfo - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Information about a gene in DBSNP (name and Entrez ID)

DBSNPGeneInfo(String, int) - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

DBSNPInfo - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Information about a DBSNP VCF file

DBSNPInfo(String, String, int, String, String) - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

DBSNPInfoFactory - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Build DBSNPInfo from a VCFHeader

DBSNPInfoFactory() - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfoFactory

DBSNPRecord - Class in de.charite.compbio.jannovar.vardbs.dbsnp

An entry in dbSNP Note that as with all databases, the annotation is for actual variants and not just positions.

DBSNPRecord(String, int, String, String, Collection<String>, Collection<String>, int, int, boolean, DBSNPVariantProperty, Collection<DBSNPGeneInfo>, int, DBSNPVariantAlleleOrigin, Collection<DBSNPVariantSuspectReasonCode>, int, String, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, Collection<Double>, boolean, Collection<String>) - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

DBSNPRecordBuilder - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Builder for DBSNPRecord class

DBSNPVariantAlleleOrigin - Enum in de.charite.compbio.jannovar.vardbs.dbsnp

Enum describing variant allele origin

DBSNPVariantProperty - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Representation of the dbSNP variant property entry.

DBSNPVariantProperty() - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantProperty

DBSNPVariantSuspectReasonCode - Enum in de.charite.compbio.jannovar.vardbs.dbsnp

Code for a variant being suspicious

DBSNPVCFHeaderExtender - Class in de.charite.compbio.jannovar.vardbs.dbsnp

Helper class for extending VCFHeaders for DBSNP annotations.

DBSNPVCFHeaderExtender(DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVCFHeaderExtender

DBVariantContextAnnotator - Class in de.charite.compbio.jannovar.vardbs.facade

Facade class for easy annotation of VariantContext objects using databases

DBVariantContextAnnotator(DBAnnotationDriver, DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator

Initialize the annotator using the given DBAnnotationDriver

DBVariantContextAnnotatorFactory - Class in de.charite.compbio.jannovar.vardbs.facade

Factory for generating DBVariantContextAnnotator objects

DBVariantContextAnnotatorFactory() - Constructor for class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotatorFactory

de.charite.compbio.jannovar - package de.charite.compbio.jannovar

de.charite.compbio.jannovar.annotation - package de.charite.compbio.jannovar.annotation

de.charite.compbio.jannovar.annotation.builders - package de.charite.compbio.jannovar.annotation.builders

de.charite.compbio.jannovar.cmd - package de.charite.compbio.jannovar.cmd

de.charite.compbio.jannovar.cmd.annotate_pos - package de.charite.compbio.jannovar.cmd.annotate_pos

de.charite.compbio.jannovar.cmd.annotate_vcf - package de.charite.compbio.jannovar.cmd.annotate_vcf

de.charite.compbio.jannovar.cmd.db_list - package de.charite.compbio.jannovar.cmd.db_list

de.charite.compbio.jannovar.cmd.download - package de.charite.compbio.jannovar.cmd.download

de.charite.compbio.jannovar.data - package de.charite.compbio.jannovar.data

de.charite.compbio.jannovar.datasource - package de.charite.compbio.jannovar.datasource

de.charite.compbio.jannovar.hgvs - package de.charite.compbio.jannovar.hgvs

de.charite.compbio.jannovar.hgvs.bridge - package de.charite.compbio.jannovar.hgvs.bridge

de.charite.compbio.jannovar.hgvs.legacy - package de.charite.compbio.jannovar.hgvs.legacy

de.charite.compbio.jannovar.hgvs.nts - package de.charite.compbio.jannovar.hgvs.nts

de.charite.compbio.jannovar.hgvs.nts.change - package de.charite.compbio.jannovar.hgvs.nts.change

de.charite.compbio.jannovar.hgvs.nts.variant - package de.charite.compbio.jannovar.hgvs.nts.variant

de.charite.compbio.jannovar.hgvs.parser - package de.charite.compbio.jannovar.hgvs.parser

de.charite.compbio.jannovar.hgvs.protein - package de.charite.compbio.jannovar.hgvs.protein

de.charite.compbio.jannovar.hgvs.protein.change - package de.charite.compbio.jannovar.hgvs.protein.change

de.charite.compbio.jannovar.hgvs.protein.variant - package de.charite.compbio.jannovar.hgvs.protein.variant

de.charite.compbio.jannovar.htsjdk - package de.charite.compbio.jannovar.htsjdk

de.charite.compbio.jannovar.impl.intervals - package de.charite.compbio.jannovar.impl.intervals

de.charite.compbio.jannovar.impl.parse - package de.charite.compbio.jannovar.impl.parse

de.charite.compbio.jannovar.impl.parse.ensembl - package de.charite.compbio.jannovar.impl.parse.ensembl

de.charite.compbio.jannovar.impl.parse.flatbed - package de.charite.compbio.jannovar.impl.parse.flatbed

de.charite.compbio.jannovar.impl.parse.gtfgff - package de.charite.compbio.jannovar.impl.parse.gtfgff

de.charite.compbio.jannovar.impl.parse.refseq - package de.charite.compbio.jannovar.impl.parse.refseq

de.charite.compbio.jannovar.impl.parse.ucsc - package de.charite.compbio.jannovar.impl.parse.ucsc

de.charite.compbio.jannovar.impl.util - package de.charite.compbio.jannovar.impl.util

de.charite.compbio.jannovar.mendel - package de.charite.compbio.jannovar.mendel

de.charite.compbio.jannovar.mendel.bridge - package de.charite.compbio.jannovar.mendel.bridge

de.charite.compbio.jannovar.mendel.filter - package de.charite.compbio.jannovar.mendel.filter

de.charite.compbio.jannovar.mendel.impl - package de.charite.compbio.jannovar.mendel.impl

de.charite.compbio.jannovar.pedigree - package de.charite.compbio.jannovar.pedigree

de.charite.compbio.jannovar.pedigree.compatibilitychecker - package de.charite.compbio.jannovar.pedigree.compatibilitychecker

de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad - package de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad

de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar - package de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar

de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd - package de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd

de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr - package de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr

de.charite.compbio.jannovar.progress - package de.charite.compbio.jannovar.progress

de.charite.compbio.jannovar.reference - package de.charite.compbio.jannovar.reference

de.charite.compbio.jannovar.vardbs.base - package de.charite.compbio.jannovar.vardbs.base

de.charite.compbio.jannovar.vardbs.dbsnp - package de.charite.compbio.jannovar.vardbs.dbsnp

de.charite.compbio.jannovar.vardbs.exac - package de.charite.compbio.jannovar.vardbs.exac

de.charite.compbio.jannovar.vardbs.facade - package de.charite.compbio.jannovar.vardbs.facade

de.charite.compbio.jannovar.vardbs.uk10k - package de.charite.compbio.jannovar.vardbs.uk10k

decrement() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

DeletionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the deletion GenomeVariants in the given TranscriptModel.

differenceTo(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

differenceTo(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

Disease - Enum in de.charite.compbio.jannovar.pedigree

Codes used to denote affection status of a person in a pedigree.

DNAUtils - Class in de.charite.compbio.jannovar.impl.util

Utility class for DNA string manipulation.

DNAUtils() - Constructor for class de.charite.compbio.jannovar.impl.util.DNAUtils

done() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

doPrint() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

doPrintProgressBars() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

DownloadCommand - Class in de.charite.compbio.jannovar.cmd.download

Implementation of download step in Jannovar.

DownloadCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommand

DownloadCommandLineParser - Class in de.charite.compbio.jannovar.cmd.download

Helper class for parsing the commandline of the download command.

DownloadCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser

Calls initializeParser().

downloadPath - Variable in class de.charite.compbio.jannovar.JannovarOptions

directory to use for the downloads and the serialized file

DuplicationChecker - Class in de.charite.compbio.jannovar.reference

Helper class for checking whether an insertion in a string is a duplication.

DuplicationChecker() - Constructor for class de.charite.compbio.jannovar.reference.DuplicationChecker

E

EnsemblParser - Class in de.charite.compbio.jannovar.impl.parse.ensembl

Parsing of ENSEMBL GTF files

EnsemblParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.Annotation

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

equals(Object) - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyChange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

equals(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

equals(Object) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

equals(Object) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

equals(Object) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.Genotype

equals(Object) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

equals(Object) - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

equals(Object) - Method in class de.charite.compbio.jannovar.pedigree.Person

equals(Object) - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

equals(Object) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

equals(Object) - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

equals(Object) - Method in class de.charite.compbio.jannovar.reference.CDSInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.CDSPosition

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

equals(Object) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

equals(Object) - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

equals(Object) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

escapeAnnField - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether or not to escape characters like '=' in the ANN VCF field.

ExacAnnotationDriver - Class in de.charite.compbio.jannovar.vardbs.exac

Annotation driver class for annotations using ExAC

ExacAnnotationDriver(String, String, DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.exac.ExacAnnotationDriver

ExacPopulation - Enum in de.charite.compbio.jannovar.vardbs.exac

Enum type for populations in the ExAC data set

ExacRecord - Class in de.charite.compbio.jannovar.vardbs.exac

Represents on entry in the ExAC VCF database file

ExacRecord(String, int, String, String, List<String>, Collection<String>, Map<ExacPopulation, List<Integer>>, Map<ExacPopulation, Integer>) - Constructor for class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

ExacRecordBuilder - Class in de.charite.compbio.jannovar.vardbs.exac

ExacVCFHeaderExtender - Class in de.charite.compbio.jannovar.vardbs.exac

Helper class for extending VCFHeaders for ExAC annotations.

ExacVCFHeaderExtender(DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.exac.ExacVCFHeaderExtender

exonIDInReferenceOrder(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns the index of the (0-based) exon in the reference (forward) order.

extendHeader(VCFHeader) - Method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

extendHeader(VCFHeader, String) - Method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

extendHeader(VCFHeader, String) - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor

Appropriately extend VCFHeader

extendHeader(VCFHeader) - Method in class de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator

Extend VCF header with the VCFHeaderExtender for the annotator

extendHeaderFields(VCFHeader, InfoFields) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

Extend a VCFHeader with the given fields.

F

FASTAParser - Class in de.charite.compbio.jannovar.impl.parse

Generic FASTA parser that allow record-wise loading of FASTA files

FASTAParser(File) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTAParser

Initialize with a file, gzip compression is automatically recognized.

FASTAParser(InputStream) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTAParser

Initialize from a InputStream, gzip compression is automatically recognized.

FASTARecord - Class in de.charite.compbio.jannovar.impl.parse

Representation of a FASTA record

FASTARecord(String, String, String) - Constructor for class de.charite.compbio.jannovar.impl.parse.FASTARecord

FeatureRecord - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Immutable class for describing a record from a GFF or GTF file.

FeatureRecord(String, String, String, int, int, String, FeatureRecord.Strand, int, Map<String, String>) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

Initialize the GFFRecord

FeatureRecord.Strand - Enum in de.charite.compbio.jannovar.impl.parse.gtfgff

Type for describing record strand

FeatureRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Abstract base class for GTF/GFF record parsers.

FeatureRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser

FileDownloadException - Exception in de.charite.compbio.jannovar.datasource

Exception that can be called if something went wrong while downloading the transcript files.

FileDownloadException() - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

FileDownloadException(String) - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

FileDownloadException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.datasource.FileDownloadException

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker

Filter list of GenotypeCalls for fitting to mode

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet

filterCompatibleRecords(Collection<GenotypeCalls>) - Method in class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom

findMatchingForPrefix(String) - Static method in enum de.charite.compbio.jannovar.hgvs.SequenceType

findOverlappingWithInterval(int, int) - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Query the encoded interval tree for all values with intervals overlapping with a given interval.

findOverlappingWithPoint(int) - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Query the encoded interval tree for all values with intervals overlapping with a given point.

FlatBEDDataSource - Class in de.charite.compbio.jannovar.datasource

A DataSource that reads regions from a BED file.

FlatBEDFastaParser - Class in de.charite.compbio.jannovar.impl.parse.flatbed

Parser for the FASTA formated files from flat BED files.

FlatBEDFastaParser(String, ArrayList<TranscriptModelBuilder>, boolean) - Constructor for class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDFastaParser

FlatBEDJannovarDataFactory - Class in de.charite.compbio.jannovar.datasource

JannovarDataFactory for flat BED files.

FlatBEDJannovarDataFactory(DatasourceOptions, DataSource, Profile.Section) - Constructor for class de.charite.compbio.jannovar.datasource.FlatBEDJannovarDataFactory

Construct the factory with the given EnsemblDataSource.

FlatBEDParser - Class in de.charite.compbio.jannovar.impl.parse.flatbed

Class for parsing flat BED data.

FlatBEDParser(ReferenceDictionary, String, Profile.Section, boolean) - Constructor for class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser

formatDuration(long) - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

fromString(String) - Static method in enum de.charite.compbio.jannovar.hgvs.VariantConfiguration

ftpProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions

proxy for FTP

G

GeneWiseMendelianAnnotationProcessor - Class in de.charite.compbio.jannovar.mendel.filter

Process VariantContext objects and annotate them with mendelian inheritance compatibility The variants put into the processor must be clustered by contig name and sorted by begin position

GeneWiseMendelianAnnotationProcessor(Pedigree, JannovarData, SAMSequenceDictionary, Consumer<VariantContext>) - Constructor for class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor

Construct processor with the path to the PED file to use

GenomeInterval - Class in de.charite.compbio.jannovar.reference

Representation of a genomic interval (chromsome, begin, end).

GenomeInterval(ReferenceDictionary, Strand, int, int, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval with zero-based coordinate system

GenomeInterval(ReferenceDictionary, Strand, int, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval with selected coordinate system

GenomeInterval(GenomeInterval) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from other with selected coordinate system

GenomeInterval(GenomeInterval, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from other with selected strand

GenomeInterval(GenomePosition, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomeInterval

construct genome interval from GenomePosition with a length towards 3' of pos' coordinate system

GenomePosition - Class in de.charite.compbio.jannovar.reference

Representation of a position on a genome (chromosome, position).

GenomePosition(ReferenceDictionary, Strand, int, int) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position with zero-based coordinate system

GenomePosition(ReferenceDictionary, Strand, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position with selected coordinate system

GenomePosition(GenomePosition) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position from other with selected coordinate system

GenomePosition(GenomePosition, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomePosition

construct genome position from other with the selected strand

GenomeRegion - Class in de.charite.compbio.jannovar.progress

A region on a genome, can be a whole chromosome

GenomeRegion(String, int, int) - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegion

GenomeRegionList - Class in de.charite.compbio.jannovar.progress

A list of GenomeRegion objects

GenomeRegionList(Iterable<GenomeRegion>) - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegionList

GenomeRegionListFactoryFromSAMSequenceDictionary - Class in de.charite.compbio.jannovar.progress

Construct GenomeRegionList from a SAMSequenceDictionary

GenomeRegionListFactoryFromSAMSequenceDictionary() - Constructor for class de.charite.compbio.jannovar.progress.GenomeRegionListFactoryFromSAMSequenceDictionary

GenomeRegionSequenceExtractor - Class in de.charite.compbio.jannovar.htsjdk

Extract sequence for a GenomeInterval from a IndexedFastaSequenceFile.

GenomeRegionSequenceExtractor(IndexedFastaSequenceFile) - Constructor for class de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor

genomeToCDSPos(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from genome position to CDS position.

genomeToTranscriptPos(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from genome position to transcript position.

GenomeVariant - Class in de.charite.compbio.jannovar.reference

Denote a change with a "REF" and an "ALT" string using genome coordinates.

GenomeVariant(GenomePosition, String, String) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object given the position, reference, and alternative nucleic acid string.

GenomeVariant(GenomePosition, String, String, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object given the position, reference, alternative nucleic acid string, and strand.

GenomeVariant(GenomeVariant, Strand) - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariant

Construct object and enforce strand.

GenomeVariantNormalizer - Class in de.charite.compbio.jannovar.reference

Helper code for the normalization of GenomeVariants.

GenomeVariantNormalizer() - Constructor for class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

GenomeVariantType - Enum in de.charite.compbio.jannovar.reference

Types of genomic variants represented by GenomeVariant.

GenomicNucleotideChangeBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Build NucleotideChange for a GenomeVariant.

GenomicNucleotideChangeBuilder(GenomeVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

Initialize with the given variant.

Genotype - Class in de.charite.compbio.jannovar.mendel

Representation of a genotype in an individual Genotypes are represented by lists of integers identifying alleles from a GenotypeCalls.

Genotype(Collection<Integer>) - Constructor for class de.charite.compbio.jannovar.mendel.Genotype

Construct Genotype with list of allele numbers

Genotype - Enum in de.charite.compbio.jannovar.pedigree

Enumeration of genotype kinds.

GenotypeBuilder - Class in de.charite.compbio.jannovar.mendel

Helper class for building Genotype objects

GenotypeBuilder() - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeBuilder

GenotypeCalls - Class in de.charite.compbio.jannovar.mendel

A list of genotypes (at an implicitely assumed site) in multiple individuals This list contains the core information for the filtration of variants by mendelian inheritance.

GenotypeCalls(ChromosomeType, Iterable<? extends Map.Entry<String, Genotype>>) - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCalls

Initialize GenotypeCalls with mapping from sample to genotype

GenotypeCalls(ChromosomeType, Iterable<? extends Map.Entry<String, Genotype>>, Object) - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCalls

Initialize GenotypeCalls with mapping from sample to genotype and an additional "payload" object

GenotypeCallsBuilder - Class in de.charite.compbio.jannovar.mendel

Helper class for building GenotypeCalls objects

GenotypeCallsBuilder() - Constructor for class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

GenotypeList - Class in de.charite.compbio.jannovar.pedigree

Deprecated.

GenotypeList(String, List<String>, boolean, ImmutableList<ImmutableList<Genotype>>) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

Construct and initialize object.

GenotypeListBuilder - Class in de.charite.compbio.jannovar.pedigree

Deprecated.

GenotypeListBuilder(String, List<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

GenotypeListBuilder(String, List<String>, boolean) - Constructor for class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

GenotypeMatch - Class in de.charite.compbio.jannovar.vardbs.base

A class for annotating the match between an observed genotype and a database genotype

GenotypeMatch(int, int, VariantContext, VariantContext) - Constructor for class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

get(int) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

get(int) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

getAA() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

getAbbreviation() - Method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getAccession() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getAccessionNumber() - Method in class de.charite.compbio.jannovar.annotation.AnnotationTextGenerator

Deprecated.

Return the accession number of the transcript associated with this variant (if possible).

getAffectedFemaleParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getAffectedMaleParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getAllCompatibleModes(List<VariantContext>) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

Method for checking whether a List of VariantContext is compatible with ALL possible modes of inheritance (UNINITIALIZED is excluded) and the given Pedigree.

getAllele() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

getAllele() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

getAlleleCounts() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getAlleleCounts(ExacPopulation) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getAlleleCounts() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getAlleleCounts() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getAlleleFrequencies() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getAlleleFrequencies(ExacPopulation) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getAlleleFrequencies() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getAlleleFrequenciesG1K() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getAlleleFrequenciesG1K() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getAlleleID() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

getAlleleNo() - Method in class de.charite.compbio.jannovar.vardbs.base.AnnotatingRecord

getAlleleNumbers() - Method in class de.charite.compbio.jannovar.mendel.Genotype

getAlleleNumbers() - Method in class de.charite.compbio.jannovar.mendel.GenotypeBuilder

getAlleles() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

getAlleles() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

getAlt() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getAlt() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getAlt() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getAlt() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getAlt() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getAlt() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getAltAlleleCounts() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getAltAlleleFrequencies() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getAltCount() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

getAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

Return mapping containing alternative gene IDs, as parsed from RefSeq GFF3 file Popular alternative identifiers (used as keys here): GeneID String of the Entrez/NCBI gene ID Genbank String of the Genbank accession HGNC String of the numeric HGNC (Human Gene Nomenclature Committee) identifier

getAltGeneIDs() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getAminoAcids() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

Get amino acid string, only available if ProteinSeqDescription.hasAminoAcids() returns true.

getAnnoLoc() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getAnnotatedMap() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Getter for all ModeOfInheritance for every variant context

getAnnotation() - Method in class de.charite.compbio.jannovar.annotation.AnnotationTextGenerator

Deprecated.

getAnnotationMessage() - Method in exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException

getAnnotations() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getAnnotations() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getAnnotator() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

getAttributes() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getBaseOffset() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

getBasePos() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

getBegin() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getBegin(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor

getBegin() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getBegin() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getBegin(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

getBeginPos() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getBeginPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getCalls() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the lists of genotype calls, each contains one entry for each individual

getCDSNTChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getCDSNTChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getCDSRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getCDSRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getCDSTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getCDSWithGenomeVariant(GenomeVariant) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Similar to TranscriptSequenceChangeHelper.getTranscriptWithChange(de.charite.compbio.jannovar.reference.GenomeVariant) but starting at the CDS begin position.

getChange() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

getChange() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

getChange() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

getChanges() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

getChanges() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

getChangeType() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

getChangeType() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

getChr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getChr() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getChr() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getChr() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getChr() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getChrID() - Method in class de.charite.compbio.jannovar.data.Chromosome

getChrName() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getChrName() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getChrName() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getChrName() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getChrom() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

getChrom() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getChrom() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getChrom() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getChrom() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getChromCount(ExacPopulation) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getChromCount() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getChromCount() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getChromCounts() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getChromCounts() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getChromosomeMap() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

getChromosomeName() - Method in class de.charite.compbio.jannovar.data.Chromosome

getChromosomes() - Method in class de.charite.compbio.jannovar.data.JannovarData

getChromType() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getChromType() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getCodonAt(TranscriptPosition, CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns the codon (String of length 3) for a change at a given position

getCodonsStartingFrom(TranscriptPosition, CDSPosition, int) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns a number of codons (String of length 3 * len) starting from the affected one by the change at txPos/cdsPos.

getCodonsStartingFrom(TranscriptPosition, CDSPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Returns all codons (String of length 3 * len) starting from the affected one by the change at txPos/cdsPos.

getComment() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getCompatibleModes() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

getCompatibleWith(List<VariantContext>) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

Method for filtering whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.

getContig() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

getContig() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getContig() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getContigID(String) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows contig name to numeric ID translation before final construction of the ReferenceDictionary.

getContigIDToLength() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getContigIDToName() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getContigLength(int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows contig length retrieval before final construction of the ReferenceDictionary.

getContigName(Integer) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Allows get contig name from a contig id.

getContigNameToID() - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

getCounter() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

getCurrentVC() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

getDataFactory() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getDataFactory() - Method in class de.charite.compbio.jannovar.datasource.FlatBEDDataSource

getDataSource(String) - Method in class de.charite.compbio.jannovar.datasource.DataSourceFactory

Construct DataSource

getDbAllele() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

getDbSNPBuildID() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

getDbSNPBuildID() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getDbSNPBuildID() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getDbSNPInfo() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPAnnotationDriver

getDBVC() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

getDefaultPrefix() - Method in class de.charite.compbio.jannovar.vardbs.base.VCFHeaderExtender

getDefaultPrefix() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVCFHeaderExtender

getDefaultPrefix() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacVCFHeaderExtender

getDefaultPrefix() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KVCFHeaderExtender

getDeletedSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

getDeletedSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

getDeletedSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

getDelSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

getDisease() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getDisease() - Method in class de.charite.compbio.jannovar.pedigree.Person

getDownloadURLs() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getDownstreamInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getEffects() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getEnd(T) - Method in interface de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor

getEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getEnd() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getEnd(TranscriptModel) - Method in class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

getEnd() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

getEndPos() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

getEndPos() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getEndPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getEndPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getEntries() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getExonRegions() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getExtraColumnHeaders() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getExtraFields() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getExtraFields() - Method in class de.charite.compbio.jannovar.pedigree.Person

getFather() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getFather() - Method in class de.charite.compbio.jannovar.pedigree.Person

getFeatureNo() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

getFileDate() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

getFileName(String) - Method in class de.charite.compbio.jannovar.datasource.DataSource

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getFilter() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getFirst() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

getFirstPos() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

getFivePrimeUTRInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns the genomic 5' UTR interval.

getFrameshift() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getFromNT() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

getFromSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

getFTPProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getGeneID() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getGeneID() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getGeneID() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getGeneInfos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getGeneInfos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getGeneName() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the name of the gene for this genotype call list

getGeneSymbol() - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the gene annotation or "." if it has no transcript.

getGeneSymbol() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getGeneSymbol() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getGeneSymbol() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getGenomeBeginPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

return the genome begin position

getGenomeEndPos() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

return the genome end position

getGenomeInterval() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getGenomePos() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getGenomeRegion(String) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

getGenomeRegions() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenomeVariant() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

Return the GenomeVariant that this AnnotationList is annotated with.

getGenomicNTChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenomicNTChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getGenotype(Person) - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext

Gets the Jannovar Genotype for a Person (name must be the same than in the VCF file)

getGenotypeBySampleNo(int) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getGenotypeForSample(String) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getGFFVersion() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

getHighestImpactAnnotation() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getHighestImpactEffect() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

Convenience method.

getHTTPProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getHTTPSProxy() - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

getID() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getId() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

getId() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getId() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getId() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getID() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getId() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getID() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getIdentifierPrefix() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

getIdx() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

getImpact() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getIndividuals() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getInfoFields() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

Getter for info fields

getInheritanceModes() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

Getter for the field inheritanceModes.

getInsertedSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

getInsSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

getIntervals() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

getIntervalsEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

getLabel() - Method in enum de.charite.compbio.jannovar.vardbs.exac.ExacPopulation

getLast() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

getLastPos() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

getLastPos() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getLeft() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getLegacyString() - Method in enum de.charite.compbio.jannovar.hgvs.legacy.LegacyLocationType

getLegacyTerm() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getLocation() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyChange

getLocation() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

getLocationType() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

getMatchedModeOfInheritances() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Getter for all possible associated ModeOfInheritance.

getMatchedModesOfInheritance() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext

getter of InheritanceVariantContext.matchedModesOfInheritance.

getMatchedVariants() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

Getter for all VariantContext that matched the ModeOfInheritance.

getMatchedVariants() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Getter for all VariantContext that matched the ModeOfInheritance.

getMax() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

getMaxCount() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

getMaxCount() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

getMaxEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getMaxEnd() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getMembers() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getMessages() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getMin() - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

getMinCount() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

getMinCount() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

getMostPathogenicVarType() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getMother() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getMother() - Method in class de.charite.compbio.jannovar.pedigree.Person

getMultiMatchBehaviour() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

getName() - Method in class de.charite.compbio.jannovar.datasource.DataSource

getName() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getName() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getName() - Method in class de.charite.compbio.jannovar.pedigree.Person

getNames() - Method in class de.charite.compbio.jannovar.datasource.DataSourceFactory

getNames() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

the list of individual names

getNames() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

the list of individual names

getNames() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNameToMember() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNameToPerson() - Method in class de.charite.compbio.jannovar.pedigree.PedFileContents

getNameToRegion() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

getNMembers() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

getNSamples() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getNucleotidePointLocation(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder

getNucleotides() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

Get nucleotidestring, only available if NucleotideSeqDescription.hasNucleotides() returns true.

getNumber() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Forward to ordinal() member function.

getNumberOfAffecteds() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getNumberOfGenes() - Method in class de.charite.compbio.jannovar.data.Chromosome

getNumberOfParents() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getNumberOfUnaffecteds() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getNumProcessed() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

getObservedAllele() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

getObsVC() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

getOffset() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

getOffset() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

getOldVariants() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getOldVariants() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getOptions() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

getOutFileName() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter

Returns output path

getOutFileName() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter

Create and return output file name.

getParentNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getParents() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getPayload() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getPayload() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getPedigree() - Method in class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

getPedigree() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

Getter for the field pedigree.

getPedigree() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getPedigree() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getPerson() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

getPhase() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getPhasing() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

getPloidy() - Method in class de.charite.compbio.jannovar.mendel.Genotype

getPos() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getPos() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getPos() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

getPos() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getPos() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getPos() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getPos() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

getPos() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getPos() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

getPos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getPos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getPos() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getPos() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getPos() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getPos() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getPosition() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

getPosition() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

getPosition() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

getPrefix() - Method in enum de.charite.compbio.jannovar.hgvs.SequenceType

getPrioritySortedList() - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

This returns an array with the VariantTypes arranged according to their priority.

getProteinChange() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getProteinChangeStr(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation

getProteinChangeStr() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getProteinID() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getProteinID() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

getPutativeImpact() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

getRange() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

getRange() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

getRange() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

getRange() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

getRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getRankType() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getRankType() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getRecord() - Method in class de.charite.compbio.jannovar.vardbs.base.AnnotatingRecord

getRef() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getRef() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

getRef() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

getRef() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getRef() - Method in interface de.charite.compbio.jannovar.reference.VariantDescription

getRef() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

getRef() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getRef() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getRef() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

getRef() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

getRef() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

getRef() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

getRefDict() - Method in class de.charite.compbio.jannovar.data.Chromosome

getRefDict() - Method in class de.charite.compbio.jannovar.data.JannovarData

getRefDict() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

getRefDict() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getRefDict() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getReference() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

getReference() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

getRefID() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getRefIDWithVersion() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getRight() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult

getRsID() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getRSID() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getRsPos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getRSPos() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getSampleNames() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getSampleToGenotype() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

getSampleToGenotype() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

getScore() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

getSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

getSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

getSeq() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

getSeq() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

getSeqDesc() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

getSeqID() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getSeqType() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getSequence() - Method in class de.charite.compbio.jannovar.impl.parse.FASTARecord

getSequence() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getSequence() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getSequenceNamePrefix() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getSequenceNamePrefix() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

getSequenceOID() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getSequenceOntologyTerm() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

getSex() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

getSex() - Method in class de.charite.compbio.jannovar.pedigree.Person

getShift() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

The shift value number of extended amino acids if positive, shift into the 5' UTR in case of negative values, or ProteinExtension.LEN_NO_TER in the case that no stop codon is encountered on the transcript.

getShiftLength() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

getSingleSampleGenotype() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext

Single Person Genotype getter.

getSource() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getSource() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

getStartCodonInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getStopCodonInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getStrand() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getStrand() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

getStrand() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

getStrand() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getStrand() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getSymbol() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

getSymbolAndAnnotation(AminoAcidCode) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the full annotation with the gene symbol.

getTargetAA() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

getTargetAA() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

getTargetAA() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

getThreePrimeUTRInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns the genomic 3' UTR interval.

getTmByAccession() - Method in class de.charite.compbio.jannovar.data.JannovarData

getTmByGeneSymbol() - Method in class de.charite.compbio.jannovar.data.JannovarData

getTMIntervalTree() - Method in class de.charite.compbio.jannovar.data.Chromosome

getToNT() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

getToSeq() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

getTotalRank() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.Annotation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTranscript() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getTranscript() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

getTranscript() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

getTranscript() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getTranscriptBeginPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscriptEndPos() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

getTranscriptStartingAtCDS() - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

getTranscriptSupportLevel() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getTranscriptSupportLevel() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getTranscriptVersion() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

getTranscriptWithChange(GenomeVariant) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Return modified transcript after applying a GenomeVariant.

getTranslator() - Static method in class de.charite.compbio.jannovar.hgvs.Translator

Factory method to get reference to Translator.

getTranslator() - Static method in class de.charite.compbio.jannovar.impl.util.Translator

Factory method to get reference to Translator.

getTXLocation() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

getTXLocation() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

getTXRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

getTXRegion() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

getType() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

getType() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

getTypeForLegacyString(String) - Static method in enum de.charite.compbio.jannovar.hgvs.legacy.LegacyLocationType

getUnaffectedNames() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

getUpstreamInterval() - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

getValue() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

getValue() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

getVarConfig() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

getVarConfig() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

getVariant() - Method in class de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder

getVariantAlleleOrigin() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getVariantAlleleOrigin() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getVariantContext() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

getVariantProperty() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getVariantProperty() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getVariantSuspectReasonCode() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getVariantSuspectReasonCode() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getVariantType() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

getVariationClass() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getVariationClass() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

getVCFHeader() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter

getVCFIdentifierPrefix() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

getVcList() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Getter for the field vcList.

getWeights() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

getWeights() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

GFFParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

A class for parsing a stream of GFFRecord objects from a GTF or GFF file.

GFFParser(File) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Initialize with a file, gzip compression is automatically recognized.

GFFParser(InputStream) - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Initialize from a InputStream, gzip compression is automatically recognized.

GFFParser.GFFVersion - Enum in de.charite.compbio.jannovar.impl.parse.gtfgff

Enum type for describing the GFF version

GFFRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Parse a line of GFF and return a FeatureRecord from this

GFFRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFRecordParser

GTFRecordParser - Class in de.charite.compbio.jannovar.impl.parse.gtfgff

Parse a line of GTF and return a FeatureRecord from this

GTFRecordParser() - Constructor for class de.charite.compbio.jannovar.impl.parse.gtfgff.GTFRecordParser

H

hasAminoAcids() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

hasAnnotation() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

hashCode() - Method in class de.charite.compbio.jannovar.annotation.Annotation

hashCode() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

hashCode() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyChange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

hashCode() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

hashCode() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

hashCode() - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

hashCode() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

hashCode() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

hashCode() - Method in class de.charite.compbio.jannovar.mendel.Genotype

hashCode() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

hashCode() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

hashCode() - Method in class de.charite.compbio.jannovar.pedigree.Person

hashCode() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

hashCode() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

hashCode() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

hashCode() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

hashCode() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

hashCode() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

hashCode() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

hasMultipleGeneSymbols() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

hasNucleotides() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

hasOnlyOneChange() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

hasOnlyOneChange() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

hasPerson(String) - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

hasStructuralVariant() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

HelpRequestedException - Exception in de.charite.compbio.jannovar.cmd

Thrown when the user requests help.

HelpRequestedException() - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException

HelpRequestedException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException

HelpRequestedException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException

HG19RefDictBuilder - Class in de.charite.compbio.jannovar.reference

Builds a ReferenceDictionary for the hg19 release.

HG19RefDictBuilder() - Constructor for class de.charite.compbio.jannovar.reference.HG19RefDictBuilder

HGVSErrorStrategy - Class in de.charite.compbio.jannovar.hgvs.parser

HGVSErrorStrategy() - Constructor for class de.charite.compbio.jannovar.hgvs.parser.HGVSErrorStrategy

HGVSLexer - Class in de.charite.compbio.jannovar.hgvs.parser

Extends the generated Antlr4HGVSLexer to bail out at the first lexing error.

HGVSLexer(CharStream) - Constructor for class de.charite.compbio.jannovar.hgvs.parser.HGVSLexer

HGVSParser - Class in de.charite.compbio.jannovar.hgvs.parser

Driver code for parsing HGVS strings into HGVSVariant objects.

HGVSParser() - Constructor for class de.charite.compbio.jannovar.hgvs.parser.HGVSParser

HGVSParser(boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.parser.HGVSParser

HGVSParsingException - Exception in de.charite.compbio.jannovar.hgvs.parser

Thrown in case of problems in HGVSParser.

HGVSParsingException() - Constructor for exception de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException

HGVSParsingException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException

HGVSParsingException(String) - Constructor for exception de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException

HGVSParsingException(Throwable) - Constructor for exception de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException

HGVSVariant - Class in de.charite.compbio.jannovar.hgvs

Base class for nucleotide and protein variants.

HGVSVariant() - Constructor for class de.charite.compbio.jannovar.hgvs.HGVSVariant

highestAlleleFreq(int) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

httpProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions

proxy for HTTP

httpsProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions

proxy for HTTPS

I

Immutable - Annotation Type in de.charite.compbio.jannovar

Annotation for marking a class as immutable.

IncompatiblePedigreeException - Exception in de.charite.compbio.jannovar.mendel

Thrown when the pedigree does not fit to the GenotypeCalls

IncompatiblePedigreeException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException

IncompatiblePedigreeException(String) - Constructor for exception de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException

increment() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

IndexedPerson(int, Person) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson

indexOf(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

indexOf(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

INFO_EFFECT - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

This line is added to the output of a VCF file annotated by Jannovar and describes the new field for the INFO section entitled EFFECT, which decribes the effects of variants (splicing,missense,stoploss, etc).

INFO_HGVS - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

This line is added to the output of a VCF file annotated by Jannovar and describes the new field for the INFO section entitled HGVS, which provides the HGVS encoded variant corresponding to the chromosomal variant in the original VCF file.

InfoFields - Enum in de.charite.compbio.jannovar.htsjdk

Describes selection of info fields.

InheritanceCompatibilityChecker - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker

Decorator for Pedigree that allows checking whether a Genotype call of a VariantContext is compatible with a selected mode of inheritance.

InheritanceCompatibilityChecker.Builder - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker

Builder for a compatibility checker.

InheritanceCompatibilityCheckerException - Exception in de.charite.compbio.jannovar.pedigree.compatibilitychecker

Exception that occurs when using invalid InheritanceVariantContextList or Pedigree objects in the compatibility checking.

InheritanceCompatibilityCheckerException() - Constructor for exception de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException

Constructor for InheritanceCompatibilityCheckerException.

InheritanceCompatibilityCheckerException(String) - Constructor for exception de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException

Constructor for InheritanceCompatibilityCheckerException.

InheritanceCompatibilityCheckerException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException

Constructor for InheritanceCompatibilityCheckerException.

InheritanceVariantContext - Class in de.charite.compbio.jannovar.pedigree

This class is an extension of VariantContext for the InheritanceCompatibilityChecker.

InheritanceVariantContextList - Class in de.charite.compbio.jannovar.pedigree

This class is a wrapper for a List of VariantContext.

InheritanceVariantContextList(List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Default constructor.

InsertionAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the insertion GenomeVariant in the given TranscriptModel

InterfaceVariantContextCompatibilityChecker - Interface in de.charite.compbio.jannovar.pedigree.compatibilitychecker

Interface for a VariantContextCompatibilityChecker.

intersection(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

Interval<T> - Class in de.charite.compbio.jannovar.impl.intervals

Half-open interval for serialization of an IntervalArray.

Interval(MutableInterval<T>) - Constructor for class de.charite.compbio.jannovar.impl.intervals.Interval

Interval(int, int, T, int) - Constructor for class de.charite.compbio.jannovar.impl.intervals.Interval

IntervalArray<T> - Class in de.charite.compbio.jannovar.impl.intervals

Sorted array of Interval objects representing an immutable interval tree.

IntervalArray(Collection<T>, IntervalEndExtractor<T>) - Constructor for class de.charite.compbio.jannovar.impl.intervals.IntervalArray

Construct object with the given values.

IntervalArray.QueryResult - Class in de.charite.compbio.jannovar.impl.intervals

Type for storing the query result.

IntervalEndExtractor<T> - Interface in de.charite.compbio.jannovar.impl.intervals

Allows extraction of begin and end position for a type.

intronRegion(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

INVALID_EXON_ID - Static variable in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

constant for invalid exon index

INVALID_INTRON_ID - Static variable in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

constant for invalid intron index

INVALID_NT_COUNT - Static variable in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

sentinel value for invalid nucleotide count

INVALID_RANK - Static variable in class de.charite.compbio.jannovar.annotation.AnnotationLocation

Sentinel value for "invalid rank".

InvalidAttributeException - Exception in de.charite.compbio.jannovar.impl.parse

InvalidAttributeException are thrown if a attribute given to a method is invalid and can not be processed.

InvalidAttributeException(String) - Constructor for exception de.charite.compbio.jannovar.impl.parse.InvalidAttributeException

InvalidCodonException - Exception in de.charite.compbio.jannovar.reference

Raised when it is attempted to access an invalid codon

InvalidCodonException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCodonException

InvalidCodonException(String) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCodonException

InvalidCoordinateException - Exception in de.charite.compbio.jannovar.reference

Thrown if two coordinates were on different chromosomes.

InvalidCoordinateException() - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCoordinateException

InvalidCoordinateException(String) - Constructor for exception de.charite.compbio.jannovar.reference.InvalidCoordinateException

InvalidCoordinatesException - Exception in de.charite.compbio.jannovar.htsjdk

Thrown in VariantContextAnnotator in the case of invalid positions (unknown chromsomes).

InvalidCoordinatesException(AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException

InvalidCoordinatesException(String, AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException

InvalidCoordinatesException(String, Throwable, AnnotationMessage) - Constructor for exception de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException

InvalidDataSourceException - Exception in de.charite.compbio.jannovar.datasource

Thrown on problems with data source configuration files.

InvalidDataSourceException() - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidDataSourceException(String) - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidDataSourceException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.datasource.InvalidDataSourceException

InvalidGenomeVariant - Exception in de.charite.compbio.jannovar.annotation

Thrown when the the given GenomeVariant does not fit the used annotation builder class.

InvalidGenomeVariant() - Constructor for exception de.charite.compbio.jannovar.annotation.InvalidGenomeVariant

InvalidGenomeVariant(String) - Constructor for exception de.charite.compbio.jannovar.annotation.InvalidGenomeVariant

IS_INTRONIC - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Predicate for testing whether a VariantEffect is intronic.

IS_SPLICING - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Predicate for testing whether a VariantEffect is related to splicing.

isAffected() - Method in class de.charite.compbio.jannovar.pedigree.Person

isAssemblyConflict() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isAssemblyConflict() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isAssemblySpecific() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isAssemblySpecific() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isAutosomal() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

whether or not the variants are on the Autosome

isBlank() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

isBlank() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

isClinicalDiagnosticAssay() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isClinicalDiagnosticAssay() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isCoding() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

isCommon() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isCommon() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isContigAlelleNotVariant() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isContigAlelleNotVariant() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isDiploid() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isDownstreamOfCDS() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

isDownstreamOfTerminal() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

isDuplication(String, String, int) - Static method in class de.charite.compbio.jannovar.reference.DuplicationChecker

isEmpty() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

isEmpty() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

isEq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isEscapeAnnField() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

isFemale() - Method in class de.charite.compbio.jannovar.pedigree.Person

isFivePercentAll() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isFivePercentAll() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isFivePercentOne() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isFivePercentOne() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isForward() - Method in enum de.charite.compbio.jannovar.reference.Strand

isFounder() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

isFounder() - Method in class de.charite.compbio.jannovar.pedigree.Person

isG1kPhase1() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isG1kPhase1() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isG1kPhase3() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isG1kPhase3() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isGenotypesAvailable() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isGenotypesAvailable() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isGeq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isGt(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isHasOMIMOrOMIA() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isHasOMIMOrOMIA() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isHet() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isHighDensityGenotyping() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isHighDensityGenotyping() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isHomAlt() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isHomRef() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isInAcceptor() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInAcceptor() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInDonor() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInDonor() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInFivePrime() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInFivePrime() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInFivePrimeUTR() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInFivePrimeUTR() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInIntron() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInIntron() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInThreePrime() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInThreePrime() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isInThreePrimeUTR() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isInThreePrimeUTR() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isIntronic() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isLeftOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

isLeftOf(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isLeftOfGap(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isLeq(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isLocusSpecificDatabase() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isLocusSpecificDatabase() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isLt(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

isMale() - Method in class de.charite.compbio.jannovar.pedigree.Person

isMatchInheritance() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContext

Getter of InheritanceVariantContext.matchedModesOfInheritance.

isMicroattributionThirdParty() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isMicroattributionThirdParty() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isMonoploid() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isMutation() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isMutation() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isNonOverlappingAlleleSet() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isNonOverlappingAlleleSet() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isNonSynonymousFrameShift() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isNonSynonymousFrameShift() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isNonSynonymousMissense() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isNonSynonymousMissense() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isNonSynonymousNonsense() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isNonSynonymousNonsense() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isNop() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

isNoTerminalExtension() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

isNoTerminalFrameshfit() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

isNotObserved() - Method in class de.charite.compbio.jannovar.mendel.Genotype

isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions

isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

isOffExome() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isOffTranscript() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isOneAnnotationOnly() - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

isOnlyPredicted() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

isOnlyPredicted() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

isOtherVariant() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isOtherVariant() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isParentOfAffected(Person) - Method in class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

isPrecious() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isPrecious() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isPubMedCentral() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isPubMedCentral() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isReference() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isReference() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isReportOverlapping() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

isReportOverlappingAsMatching() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

isReverse() - Method in enum de.charite.compbio.jannovar.reference.Strand

isReversed() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isReversed() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isRightOf(int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

isRightOf(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isRightOfGap(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

isShort() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

isSplicing() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isStructural() - Method in enum de.charite.compbio.jannovar.annotation.VariantEffect

isSubmitterLinkOut() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isSubmitterLinkOut() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isSymbolic() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

isSynonymous() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isSynonymous() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isThirdPartyAnnotation() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isThirdPartyAnnotation() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isThreeDStructure() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isThreeDStructure() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isTopPriorityVariant() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

We do not know, actually, whether any given variant is pathogenic if we just judge its pathogenicity class.

isTransition() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

A transition is between purine and purine or between pyrimidine and pyrimidine.

isTransversion() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

A transversion is purine <-> pyrimidine.

isUnaffected() - Method in class de.charite.compbio.jannovar.pedigree.Person

isValidated() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isValidated() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isWithdrawn() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

isWithdrawn() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

isXChromosomal() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

whether or not the variants are on the X chromsome

isXChromosomal() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

whether or not the variants are on the X chromsome

iterator() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

iterator() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

iterator() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

J

Jannovar - Class in de.charite.compbio.jannovar

This is the driver class for a program called Jannovar.

Jannovar() - Constructor for class de.charite.compbio.jannovar.Jannovar

JANNOVAR_VERSION - Static variable in class de.charite.compbio.jannovar.JannovarOptions

the version of the program

JannovarAnnotationCommand - Class in de.charite.compbio.jannovar.cmd

Base class for commands needing annotation data.

JannovarAnnotationCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand

JannovarAnnotationCommandLineParser - Class in de.charite.compbio.jannovar.cmd

Base class for the command line parser for the annotation commands.

JannovarAnnotationCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser

Calls initializeParser().

JannovarCommand - Class in de.charite.compbio.jannovar.cmd

Super class for all commands, i.e.

JannovarCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.JannovarCommand

Initialize the JannovarCommand.

JannovarData - Class in de.charite.compbio.jannovar.data

This data type is used for serialization after downloading.

JannovarData(ReferenceDictionary, ImmutableList<TranscriptModel>) - Constructor for class de.charite.compbio.jannovar.data.JannovarData

Initialize the object with the given values.

JannovarDataFactory - Class in de.charite.compbio.jannovar.datasource

Interface for data factories, allowing to create JannovarData objects from DataSources.

JannovarDataFactory(DatasourceOptions, DataSource, Profile.Section) - Constructor for class de.charite.compbio.jannovar.datasource.JannovarDataFactory

Construct the factory with the given DataSource.

JannovarDataSerializer - Class in de.charite.compbio.jannovar.data

Manager for serializing and deserializing JannovarData objects.

JannovarDataSerializer(String) - Constructor for class de.charite.compbio.jannovar.data.JannovarDataSerializer

Initialize the (de)serializer with the path to the file to load/save.

JannovarException - Exception in de.charite.compbio.jannovar

Base class for exceptions in Jannovar.

JannovarException() - Constructor for exception de.charite.compbio.jannovar.JannovarException

JannovarException(String) - Constructor for exception de.charite.compbio.jannovar.JannovarException

JannovarException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.JannovarException

JannovarOptions - Class in de.charite.compbio.jannovar

Configuration for the Jannovar program.

JannovarOptions() - Constructor for class de.charite.compbio.jannovar.JannovarOptions

JannovarOptions.Command - Enum in de.charite.compbio.jannovar

The command that is to be executed.

JannovarVarDBException - Exception in de.charite.compbio.jannovar.vardbs.base

Raised on problems with variant database annotation

JannovarVarDBException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.vardbs.base.JannovarVarDBException

JannovarVarDBException(String) - Constructor for exception de.charite.compbio.jannovar.vardbs.base.JannovarVarDBException

join(String...) - Static method in class de.charite.compbio.jannovar.impl.util.PathUtil

Join file name components.

K

key() - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

key(String) - Static method in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

L

lastIndexOf(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

lastIndexOf(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

LegacyChange - Class in de.charite.compbio.jannovar.hgvs.legacy

Base class for legacy changes.

LegacyChange(LegacyLocation) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyChange

Initialize members with the given parameters

LegacyChangeParser - Class in de.charite.compbio.jannovar.hgvs.parser

Parser for legacy change syntax (starting with "IVS", "EX", or "E").

LegacyChangeParser() - Constructor for class de.charite.compbio.jannovar.hgvs.parser.LegacyChangeParser

LegacyChangeParser(boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.parser.LegacyChangeParser

LegacyDeletion - Class in de.charite.compbio.jannovar.hgvs.legacy

Representation of a legacy notation deletion.

LegacyDeletion(LegacyLocation, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

Construct new legacy deletion with the given values

LegacyIndel - Class in de.charite.compbio.jannovar.hgvs.legacy

Representation of a legacy notation substitution.

LegacyIndel(LegacyLocation, NucleotideSeqDescription, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

Construct new legacy substitution with the given values

LegacyInsertion - Class in de.charite.compbio.jannovar.hgvs.legacy

Representation of a legacy notation insertion.

LegacyInsertion(LegacyLocation, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

Construct new legacy substitution with the given values

LegacyLocation - Class in de.charite.compbio.jannovar.hgvs.legacy

Exonic location for legacy variants, e.g.

LegacyLocation(LegacyLocationType, int, int) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

Initialize object with the given values

LegacyLocationType - Enum in de.charite.compbio.jannovar.hgvs.legacy

Enum describing either intronic or exonic locations.

LegacySubstitution - Class in de.charite.compbio.jannovar.hgvs.legacy

Representation of a legacy notation substitution.

LegacySubstitution(LegacyLocation, String, String) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

Construct new legacy substitution with the given values

LegacyVariant - Class in de.charite.compbio.jannovar.hgvs.legacy

Representation of a LegacyChange on a reference sequence.

LegacyVariant(String, LegacyChange) - Constructor for class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

Initialize object with the given values

LEN_NO_TER - Static variable in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

no terminal is encountered

LEN_NO_TER - Static variable in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

no terminal is encountered

LEN_SHORT - Static variable in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

short change description

length() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

length() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

length() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

length() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

length() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

returns length of the interval

length() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

returns length of the interval

length() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

lengthUpTo(String, int) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

liesInCDS(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInCDSIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInDownstreamRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within with the downstream region of the transcript.

liesInExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInFivePrimeUTR(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInSpliceAcceptorSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice acceptor site.

liesInSpliceDonorSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice donor site.

liesInSpliceRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within a splice region.

liesInThreePrimeUTR(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInTranslationalStartSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInTranslationalStopSite(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

liesInUpstreamRegion(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given pos lies within with the upstream region of the transcript.

listIterator() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

listIterator(int) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

listIterator() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

listIterator(int) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

load() - Method in class de.charite.compbio.jannovar.data.JannovarDataSerializer

Deserialize a JannovarData object from a file.

load(GenomeInterval) - Method in class de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor

Load sequence from the given region from GenomeRegionSequenceExtractor.indexedFile

locateExon(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

locateExon(TranscriptPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

locateIntron(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Returns (0-based) index of the intron (in the order determined by the transcript's strand).

LONGEST_TRANSCRIPT - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Longest transcript of a gene (used in absence of any TSL annotation and UCSC annotation of this transcript).

LOW_PRIORITY - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Lowest available priority (used in absence of any TSL and UCSC annotation of this transcript).

M

main(String[]) - Static method in class de.charite.compbio.jannovar.Jannovar

makeSingleChangeVariant(SequenceType, String, NucleotideChange) - Static method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

makeSingleChangeVariant(String, ProteinChange) - Static method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

matchGenotypes(VariantContext, VariantContext) - Method in class de.charite.compbio.jannovar.vardbs.base.AlleleMatcher

Match genotypes of two VariantContexts Indels will be left-shifted and normalized when necessary

MendelianCheckerAD - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal dominant case

MendelianCheckerAD(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD

MendelianCheckerAR - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal recessive case

MendelianCheckerAR(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR

MendelianCheckerARCompoundHet - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a Collection of GenotypeCalls for compatibility with a Pedigree and autosomal recessive compound het mode of inheritance.

MendelianCheckerARCompoundHet(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet

MendelianCheckerARHom - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a Collection of GenotypeCalls for compatibility with a Pedigree and autosomal recessive homozygous mode of inheritance.

MendelianCheckerARHom(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom

MendelianCheckerXD - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal dominant case

MendelianCheckerXD(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD

MendelianCheckerXR - Class in de.charite.compbio.jannovar.mendel.impl

Implementation of Mendelian compatibility check for autosomal recessive case

MendelianCheckerXR(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR

MendelianCheckerXRCompoundHet - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a GenotypeCalls for compatibility with a Pedigree and X recessive compound het.

MendelianCheckerXRCompoundHet(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet

MendelianCheckerXRHom - Class in de.charite.compbio.jannovar.mendel.impl

Helper class for checking a GenotypeCalls for compatibility with a Pedigree and AR homozygous mode

MendelianCheckerXRHom(MendelianInheritanceChecker) - Constructor for class de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom

MendelianInheritanceChecker - Class in de.charite.compbio.jannovar.mendel

Facade class for checking lists of GenotypeCalls for compatibility with mendelian inheritance

MendelianInheritanceChecker(Pedigree) - Constructor for class de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker

Construct checker with the pedigree to use

MendelVCFHeaderExtender - Class in de.charite.compbio.jannovar.mendel.bridge

Helper class for extending VCF header for mendelian inheritance annotation

MendelVCFHeaderExtender() - Constructor for class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

ModeOfInheritance - Enum in de.charite.compbio.jannovar.mendel

An enumeration of the four main Mendelian modes of inheritance for prioritizing exome data

MultiAlleleNucleotideVariant - Class in de.charite.compbio.jannovar.hgvs.nts.variant

Nucleotide variant having multiple alleles.

MultiAlleleNucleotideVariant(SequenceType, String, String, int, Collection<NucleotideChangeAllele>) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

Construct with the given SequenceType, reference/transcript ID, protein ID, transcript version, and collection of NucleotideChangeAlleles.

MultiAlleleNucleotideVariant(SequenceType, String, Collection<NucleotideChangeAllele>) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

Construct with the given SequenceType, reference/transcript ID and collection of NucleotideChangeAlleles.

MultiAlleleProteinVariant - Class in de.charite.compbio.jannovar.hgvs.protein.variant

Protein variant having multiple alleles.

MultiAlleleProteinVariant(String, Collection<ProteinChangeAllele>) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

Construct with the given protein ID and collection of ProteinChangeAlleles.

MutableInterval<T> - Class in de.charite.compbio.jannovar.impl.intervals

Mutable half-open interval, for incremental building of Interval objects.

MutableInterval() - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

MutableInterval(int, int, T, int) - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

MutableInterval(int, int, T) - Constructor for class de.charite.compbio.jannovar.impl.intervals.MutableInterval

N

namesEqual(Pedigree) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

Check whether the GenotypeList.names of this GenotypeCalls are the same as the names of the members of pedigree.

namesEqual(Pedigree) - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

Check whether the InheritanceVariantContextList.names of this GenotypeCalls are the same as the names of the members of pedigree.

next() - Method in class de.charite.compbio.jannovar.impl.parse.FASTAParser

Reads next record from the GFF file and return it, null when the file is at its end.

next() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser

Reads next record from the GFF file and return it, null when the file is at its end.

NO_CALL - Static variable in class de.charite.compbio.jannovar.mendel.Genotype

NO_PROTEIN_ISOFORM - Static variable in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

NO_TRANSCRIPT_VERSION - Static variable in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

normalizeDeletion(String, AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Normalize deletion AminoAcidChange for amino acid string Return change if it is not a clean deletion.

normalizeDeletion(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform a deletion GenomeVariant into its HGVS-normalized representation.

normalizeGenomeChange(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform a GenomeVariant to its HGVS-normalized representation.

normalizeInsertion(TranscriptModel, GenomeVariant, TranscriptPosition) - Static method in class de.charite.compbio.jannovar.reference.GenomeVariantNormalizer

Transform an insertion GenomeVariant to its HGVS-normalized representation.

normalizeInsertion(VariantDescription) - Method in class de.charite.compbio.jannovar.vardbs.base.VariantNormalizer

Normalize a variant given as a start coordinate, reference, and variant sequence However, leave the leftmost base intact in the case so insertions have a REF base.

normalizeVariant(VariantDescription) - Method in class de.charite.compbio.jannovar.vardbs.base.VariantNormalizer

Normalize a variant given as a start coordinate, reference, and variant sequence The chromosome is given by its name, position is an 0-based integer, reference and variant are given as sequence.

NOT_AVAILABLE - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version)

nt3PrimeShifting - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether or not to shift variants towards the 3' end of the transcript

NucleotideChange - Class in de.charite.compbio.jannovar.hgvs.nts.change

Base class for nucleotide changes.

NucleotideChange(boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

NucleotideChangeAllele - Class in de.charite.compbio.jannovar.hgvs.nts.variant

Contains the NucleotideChanges on one allee.

NucleotideChangeAllele(VariantConfiguration, Collection<? extends NucleotideChange>) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Construct allele with the given a variant VariantConfiguration and NucleotideChanges.

NucleotideChangeToGenomeVariantTranslationImplBase - Class in de.charite.compbio.jannovar.hgvs.bridge

NucleotideChangeToGenomeVariantTranslationImplBase(GenomeRegionSequenceExtractor) - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslationImplBase

NucleotideChangeToGenomeVariantTranslator - Class in de.charite.compbio.jannovar.hgvs.bridge

Helper for converting a NucleotideChange to a GenomeVariant.

NucleotideChangeToGenomeVariantTranslator(JannovarData, IndexedFastaSequenceFile) - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator

NucleotideDeletion - Class in de.charite.compbio.jannovar.hgvs.nts.change

Deletion in a nucleotide sequence.

NucleotideDeletion(boolean, NucleotideRange, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

NucleotideDuplication - Class in de.charite.compbio.jannovar.hgvs.nts.change

Representation of a duplication on the nucleotide level.

NucleotideDuplication(boolean, NucleotideRange, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

NucleotideIndel - Class in de.charite.compbio.jannovar.hgvs.nts.change

NucleotideIndel(boolean, NucleotideRange, NucleotideSeqDescription, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

NucleotideInsertion - Class in de.charite.compbio.jannovar.hgvs.nts.change

Insertion into a Nucleotide sequence.

NucleotideInsertion(boolean, NucleotideRange, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

NucleotideInversion - Class in de.charite.compbio.jannovar.hgvs.nts.change

NucleotideInversion(boolean, NucleotideRange, NucleotideSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

NucleotideLocationConverter - Class in de.charite.compbio.jannovar.hgvs.bridge

Helper class for converting NucleotidePointLocations and NucleotideRanges to GenomePositions and GenomeIntervals.

NucleotideLocationConverter() - Constructor for class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter

NucleotideMiscChange - Class in de.charite.compbio.jannovar.hgvs.nts.change

Represents a silent protein-level change, i.e., "p.=".

NucleotideMiscChange(boolean, NucleotideMiscChangeType) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

Construct with given changeType and onlyPredicted flag.

NucleotideMiscChangeType - Enum in de.charite.compbio.jannovar.hgvs.nts.change

Enumeration of the miscellaneous nucleotide change types (for RNA).

NucleotidePointLocation - Class in de.charite.compbio.jannovar.hgvs.nts

Position in a nucleotide string.

NucleotidePointLocation(int) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

Deprecated.

NucleotidePointLocation(int, int, boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

Construct with given base position and offset

NucleotidePointLocationBuilder - Class in de.charite.compbio.jannovar.reference

Helper class that allows easy building of NucleotidePointLocations.

NucleotidePointLocationBuilder(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder

Construct the position builder with the given transcript

NucleotideRange - Class in de.charite.compbio.jannovar.hgvs.nts

Range in a nucleotide sequence.

NucleotideRange(NucleotidePointLocation, NucleotidePointLocation) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

NucleotideSeqDescription - Class in de.charite.compbio.jannovar.hgvs.nts

Specification for a nucleotide sequence, e.g.

NucleotideSeqDescription() - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

Construct as reporting the empty string.

NucleotideSeqDescription(int) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

Construct with nucleotide string length and null string.

NucleotideSeqDescription(String) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

Construct with nucleotide string length.

NucleotideShortSequenceRepeatVariability - Class in de.charite.compbio.jannovar.hgvs.nts.change

NucleotideShortSequenceRepeatVariability(boolean, NucleotideRange, int, int) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

Construct with the given values

NucleotideSubstitution - Class in de.charite.compbio.jannovar.hgvs.nts.change

Substitution of one nucleotide.

NucleotideSubstitution(boolean, NucleotidePointLocation, String, String) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

Construct with the given values

nucleotidesWithInsertion(String, int, String) - Static method in class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

Insert the string in insertion at the position given by frameShift in the given codon string transcriptCodon to targetNC and return the updated nucleic string.

NucleotideVariant - Class in de.charite.compbio.jannovar.hgvs.nts.variant

Base class for nucleotide changes.

NucleotideVariant(SequenceType, String) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

Set variant's reference ID, protein ID is null, version is NucleotideVariant.NO_TRANSCRIPT_VERSION

NucleotideVariant(SequenceType, String, String, int) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

Set variant's reference ID, protein ID, and protein version to the given value

O

OldVariantType - Enum in de.charite.compbio.jannovar.annotation

Enumeration of the old Jannovar variant types (i.e.

openVariantContextWriter(VCFHeader, OutputStream, InfoFields, Collection<VCFHeaderLine>) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields).

openVariantContextWriter(VCFHeader, String, InfoFields, Collection<VCFHeaderLine>) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields).

openVariantContextWriter(VCFHeader, String, InfoFields, Collection<VCFHeaderLine>, boolean) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

Return a new VariantContextWriter that uses the header from reader but has the header extended header through VariantContextWriterConstructionHelper.extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields).

openVariantContextWriter(VCFHeader, String, InfoFields) - Static method in class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

Forward to VariantContextWriterConstructionHelper.openVariantContextWriter(VCFHeader, String, InfoFields, Collection).

Options() - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

Constructor

Options(InfoFields, boolean, boolean, boolean) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

constructor using fields

outputInfix - Variable in class de.charite.compbio.jannovar.JannovarOptions

infix added to output file name before .vcf/.vcf.gz/.bcf output

outVCFFile - Variable in class de.charite.compbio.jannovar.JannovarOptions

path to output VCF file path (overrides generation of file name from input file name)

outVCFFolder - Variable in class de.charite.compbio.jannovar.JannovarOptions

path to output folder for the annotated VCF files (default is parallel to input file)

overlapsWith(int, int) - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

overlapsWith(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

overlapsWith(VariantDescription) - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

overlapsWithCDS(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithCDSExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithCDSIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithDownstreamRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with the downstream region of the transcript.

overlapsWithExon(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithFivePrimeUTR(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithIntron(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithSpliceAcceptorSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice acceptor site.

overlapsWithSpliceDonorSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice donor site.

overlapsWithSpliceRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with a splice region.

overlapsWithThreePrimeUTR(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithTranslationalStartSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithTranslationalStopSite(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

overlapsWithUpstreamRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Returns whether the given interval overlaps with the upstream region of the transcript.

P

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser

Parse the command line and

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser

Parse the command line and

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser

Parse command line arguments and return JannovarOptions.

parse() - Method in class de.charite.compbio.jannovar.impl.parse.ReferenceDictParser

Load accessions and chromInfo file and return resulting ReferenceDictionary.

parseHGVSString(String) - Method in class de.charite.compbio.jannovar.hgvs.parser.HGVSParser

Parse HGVS change string

parseLegacyChangeString(String) - Method in class de.charite.compbio.jannovar.hgvs.parser.LegacyChangeParser

Parse legacy change

parseLine(String) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser

Parse the line and return the corresponding FeatureRecord

parseTranscriptModelFromLine(String) - Method in class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

The function parses a single line of the knownGene.txt file.

pathFASTARef - Variable in class de.charite.compbio.jannovar.JannovarOptions

Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation

pathPedFile - Variable in class de.charite.compbio.jannovar.JannovarOptions

Path to pedigree file

PathUtil - Class in de.charite.compbio.jannovar.impl.util

Utility class with static methods for path manipulation.

PathUtil() - Constructor for class de.charite.compbio.jannovar.impl.util.PathUtil

pathVCFDBSNP - Variable in class de.charite.compbio.jannovar.JannovarOptions

Path to dbSNP VCF file to use for the annotation

pathVCFExac - Variable in class de.charite.compbio.jannovar.JannovarOptions

Path to ExAC VCF file to use for the annotation

pathVCFUK10K - Variable in class de.charite.compbio.jannovar.JannovarOptions

Path to UK10K VCF file to use for the annotation

PedFileContents - Class in de.charite.compbio.jannovar.pedigree

Represents the contents of a pedigree file.

PedFileContents(ImmutableList<String>, ImmutableList<PedPerson>) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileContents

PedFileReader - Class in de.charite.compbio.jannovar.pedigree

Allows reading of PedFileContents from a InputStream or File.

PedFileReader(File) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileReader

Initialize object with the given file.

PedFileWriter - Class in de.charite.compbio.jannovar.pedigree

Allows writing of PedFileContents to a OutputStream or File.

PedFileWriter(File) - Constructor for class de.charite.compbio.jannovar.pedigree.PedFileWriter

pedigree(Pedigree) - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder

Set the pedigree for the builder

Pedigree - Class in de.charite.compbio.jannovar.pedigree

Represent one pedigree from a PED file.

Pedigree(String, Collection<Person>) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree

Initialize the object with the given values

Pedigree(PedFileContents, String) - Constructor for class de.charite.compbio.jannovar.pedigree.Pedigree

Initialize the object with the members of contents that have the pedigree name equal to pedigreeName.

Pedigree.IndexedPerson - Class in de.charite.compbio.jannovar.pedigree

Helper class, used in the name to member map.

PedigreeExtractor - Class in de.charite.compbio.jannovar.pedigree

Helper class for extracting one family from a PedFileContents object.

PedigreeExtractor(String, PedFileContents) - Constructor for class de.charite.compbio.jannovar.pedigree.PedigreeExtractor

PedigreeQueryDecorator - Class in de.charite.compbio.jannovar.pedigree

Decorator of Pedigree that allows for the easy querying.

PedigreeQueryDecorator(Pedigree) - Constructor for class de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator

Initialize decorator.

PedParseException - Exception in de.charite.compbio.jannovar.pedigree

Exception that occurs during parsing of PEDfiles.

PedParseException() - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedParseException(String) - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedParseException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.pedigree.PedParseException

PedPerson - Class in de.charite.compbio.jannovar.pedigree

Representation of a line from a pedigree (.ped) file.

PedPerson(String, String, String, String, Sex, Disease, Collection<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.PedPerson

Initialize object with the given data.

PedPerson(String, String, String, String, Sex, Disease) - Constructor for class de.charite.compbio.jannovar.pedigree.PedPerson

Initialize object with the given data.

Person - Class in de.charite.compbio.jannovar.pedigree

An individual from a pedigree file, Java programmer friendly version.

Person(String, Person, Person, Sex, Disease, Collection<String>) - Constructor for class de.charite.compbio.jannovar.pedigree.Person

Initialize object with the given values.

Person(String, Person, Person, Sex, Disease) - Constructor for class de.charite.compbio.jannovar.pedigree.Person

Initialize object with the given values and empty extra fields list.

popWithHighestAlleleFreq(int) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

positionOverlaps(VariantContext, VariantContext) - Method in class de.charite.compbio.jannovar.vardbs.base.AlleleMatcher

Pair genotypes of two VariantContexts based on their position, regardless of their genotype In the end, all genotypes will be matched regardless of matching alleles, such that later the "best" (e.g., the highest frequency one) can be used for annotating a variant.

PositionType - Enum in de.charite.compbio.jannovar.reference

Enum for differentiating between one- and zero-based positions.

prefixDBSNP - Variable in class de.charite.compbio.jannovar.JannovarOptions

Prefix to use for dbSNP VCF INFO Fields

prefixExac - Variable in class de.charite.compbio.jannovar.JannovarOptions

Prefix to use for ExAC VCF INFO Fields

prefixUK10K - Variable in class de.charite.compbio.jannovar.JannovarOptions

Prefix to use for UK10K VCF INFO Fields

print(PrintStream) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionary

Print dictionary to System.err for debugging purposes.

print(long) - Method in class de.charite.compbio.jannovar.impl.util.ProgressBar

print progress up to position pos, if ProgressBar.doPrint

print(PrintStream) - Method in class de.charite.compbio.jannovar.JannovarOptions

Print option values to stderr.

print() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

printHeader() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

printHelp() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser

printProgressBars - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether to print progress bars to stderr or not.

priorityLevel() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

The preference level for annotations is exonic (1): FS_DELETION, FS_INSERTION, NON_FS_SUBSTITUTION, FS_SUBSTITUTION, MISSENSE, NON_FS_DELETION, NON_FS_INSERTION, STOPGAIN, STOPLOSS, FS_DUPLICATION, NON_FS_DUPLICATION, START_LOSS, START_GAIN.

ProgressBar - Class in de.charite.compbio.jannovar.impl.util

A simple status bar that only work on terminals where "\r" has an affect.

ProgressBar(long, long) - Constructor for class de.charite.compbio.jannovar.impl.util.ProgressBar

Initialize progress bar with the given settings

ProgressBar(long, long, boolean) - Constructor for class de.charite.compbio.jannovar.impl.util.ProgressBar

Initialize progress bar with the given settings

ProgressReporter - Class in de.charite.compbio.jannovar.progress

Helper for displaying progress

ProgressReporter(GenomeRegionList, int) - Constructor for class de.charite.compbio.jannovar.progress.ProgressReporter

projectGenomeToCDSInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomeInterval to CDSInterval for TranscriptProjectionDecorator.transcript.

projectGenomeToCDSPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomePosition to CDSPosition for TranscriptProjectionDecorator.transcript.

projectGenomeToTXInterval(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomeInterval to TranscriptInterval for TranscriptProjectionDecorator.transcript.

projectGenomeToTXPosition(GenomePosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Translate GenomePosition to TranscriptPosition for TranscriptProjectionDecorator.transcript.

ProjectionException - Exception in de.charite.compbio.jannovar.reference

Thrown when a coordinate conversion failed.

ProjectionException(String) - Constructor for exception de.charite.compbio.jannovar.reference.ProjectionException

ProteinChange - Class in de.charite.compbio.jannovar.hgvs.protein.change

Base class for protein changes.

ProteinChange(boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

ProteinChangeAllele - Class in de.charite.compbio.jannovar.hgvs.protein.variant

Contains the ProteinChanges on one allee.

ProteinChangeAllele(VariantConfiguration, Collection<? extends ProteinChange>) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Construct allele with the given a variant VariantConfiguration and ProteinChanges.

ProteinDeletion - Class in de.charite.compbio.jannovar.hgvs.protein.change

In-frame deletion of a protein (i.e., without frameshift, but can destroy codons).

ProteinDeletion(boolean, ProteinRange) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion without length and sequence information

ProteinDeletion(boolean, ProteinRange, int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion with length information

ProteinDeletion(boolean, ProteinRange, String) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

Construct ProteinDeletion with sequence information

ProteinDuplication - Class in de.charite.compbio.jannovar.hgvs.protein.change

ProteinDuplication(boolean, ProteinRange, ProteinSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

ProteinExtension - Class in de.charite.compbio.jannovar.hgvs.protein.change

ProteinExtension(boolean, ProteinPointLocation, String, int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

Construct ProteinExtension with the given values

ProteinFrameshift - Class in de.charite.compbio.jannovar.hgvs.protein.change

Protein frame shift change.

ProteinFrameshift(boolean, ProteinPointLocation, String, int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

Construct ProteinFrameshift with the given values

ProteinIndel - Class in de.charite.compbio.jannovar.hgvs.protein.change

In-frame substitution on the protein level with more than one base.

ProteinIndel(boolean, ProteinRange, ProteinSeqDescription, ProteinSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

ProteinInsertion - Class in de.charite.compbio.jannovar.hgvs.protein.change

Insertion into a protein sequence.

ProteinInsertion(boolean, ProteinRange, ProteinSeqDescription) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

ProteinMiscChange - Class in de.charite.compbio.jannovar.hgvs.protein.change

Represents a silent protein-level change, i.e., "p.=".

ProteinMiscChange(boolean, ProteinMiscChangeType) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

Construct with given changeType and onlyPredicted flag.

ProteinMiscChangeType - Enum in de.charite.compbio.jannovar.hgvs.protein.change

Enum with for the miscellaneous protein changes.

ProteinPointLocation - Class in de.charite.compbio.jannovar.hgvs.protein

Represent one position in a protein.

ProteinPointLocation(String, int, int, boolean) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

ProteinRange - Class in de.charite.compbio.jannovar.hgvs.protein

Represent a range in a protein.

ProteinRange(ProteinPointLocation, ProteinPointLocation) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

ProteinSeqDescription - Class in de.charite.compbio.jannovar.hgvs.protein

Specification for inserted protein sequence, e.g.

ProteinSeqDescription() - Constructor for class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

Construct as reporting the empty string.

ProteinSeqDescription(int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

Construct with amino acid string length and null string.

ProteinSeqDescription(String) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

Construct with amino acid string length.

ProteinShortSequenceRepeatVariability - Class in de.charite.compbio.jannovar.hgvs.protein.change

Describes short sequence repeat (SSR) variability.

ProteinShortSequenceRepeatVariability(boolean, ProteinRange, int, int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

Construct with the given values

ProteinSubstitution - Class in de.charite.compbio.jannovar.hgvs.protein.change

Represents a missense protein substitution, for example "Trp2Ala" or "T2A".

ProteinSubstitution(boolean, ProteinPointLocation, String) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

ProteinVariant - Class in de.charite.compbio.jannovar.hgvs.protein.variant

Base class for protein changes.

ProteinVariant(String) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

Set variant's reference ID, protein ID is null, isoform is ProteinVariant.NO_PROTEIN_ISOFORM.

ProteinVariant(String, String, int) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

Set variant's reference ID, protein ID, and protein isoform to the given value

put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter

Write out the given VariantContext with additional annotation.

put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter

put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor

put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker

put(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor

put(VariantContext) - Method in interface de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor

Put a Variant Context into the filter.

PutativeImpact - Enum in de.charite.compbio.jannovar.annotation

Putative impact of an annotation.

putContigID(String, int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Add a contig name to numeric ID mapping to builder.

putContigLength(int, int) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Add a contig id to length mapping.

putContigName(int, String) - Method in class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

Set primary contig ID to name mapping.

putErrorAnnotation(VariantContext, Set<AnnotationMessage>) - Method in class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Put error annotation messages to a VariantContext into the ANN field in the INFO column.

R

rank - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.rank of next build AnnotationLocation.

rankType - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.rankType of next build AnnotationLocation.

read() - Method in class de.charite.compbio.jannovar.pedigree.PedFileReader

Read in the pedigree file in PedFileReader.file.

read(InputStream) - Static method in class de.charite.compbio.jannovar.pedigree.PedFileReader

Static method for parsing a PED file into a PedFileContents object.

recover(LexerNoViableAltException) - Method in class de.charite.compbio.jannovar.hgvs.parser.HGVSLexer

REF_CALL - Static variable in class de.charite.compbio.jannovar.mendel.Genotype

ReferenceDictionary - Class in de.charite.compbio.jannovar.data

Stores lengths of contigs/chromosomes and a mapping from string to numeric IDs.

ReferenceDictionaryBuilder - Class in de.charite.compbio.jannovar.data

Builder class for incremental building of immutable ReferenceDictionary objects.

ReferenceDictionaryBuilder() - Constructor for class de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

ReferenceDictParser - Class in de.charite.compbio.jannovar.impl.parse

Allows loading of ReferenceDictParser from UCSC and RefSeq data.

ReferenceDictParser(String, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ReferenceDictParser

Initialize the parser with the paths to the file to parse.

RefSeqParser - Class in de.charite.compbio.jannovar.impl.parse.refseq

Parsing of RefSeq GFF3 files

RefSeqParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser

remove(Object) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

remove(int) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

remove(Object) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

remove(int) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

removeAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

removeAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

reset() - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

Reset the builder into the state after initialization.

retainAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

retainAll(Collection<?>) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

reverseComplement(String) - Static method in class de.charite.compbio.jannovar.impl.util.DNAUtils

Return the reverse complement version of a DNA string in upper case.

run() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand

This function will simply annotate given chromosomal position with HGVS compliant output.

run() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand

This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file with the suffix .de.charite.compbio.jannovar).

run() - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand

Perform the downloading.

run() - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommand

Perform the downloading.

run() - Method in class de.charite.compbio.jannovar.cmd.JannovarCommand

Function for the execution of the command.

run() - Method in class de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser

run() - Method in class de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser

run() - Method in class de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser

run() - Method in interface de.charite.compbio.jannovar.impl.parse.TranscriptParser

run(Collection<TranscriptModelBuilder>) - Static method in class de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths

run() - Method in class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

run() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

run() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant

run() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive

run() - Method in interface de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker

run.

run() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

run() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive

run() - Method in class de.charite.compbio.jannovar.pedigree.PedigreeExtractor

Invoke extraction of the given pedigree from contents used in construction.

run() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

runMultiSampleCase() - Method in interface de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker

All variants of the InheritanceVariantContextList that are compatible with Pedigree and the mode of inheritances will be set true for their compatibility.

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

runMultiSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

runSingleSampleCase() - Method in interface de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker

All variants of the InheritanceVariantContextList that are compatible with index (first individual of the VCF file) and the mode of inheritances will be set true for their compatibility

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

runSingleSampleCase() - Method in class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive

S

save(JannovarData) - Method in class de.charite.compbio.jannovar.data.JannovarDataSerializer

Serialize a JannovarData object to a file.

SequenceType - Enum in de.charite.compbio.jannovar.hgvs

Type of the sequence that the variant is on.

SerializationException - Exception in de.charite.compbio.jannovar.data

Exception thrown on problems with serialization or deserialization.

SerializationException(String) - Constructor for exception de.charite.compbio.jannovar.data.SerializationException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.annotation.AnnotationException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.JannovarException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.pedigree.PedParseException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.reference.ProjectionException

serialVersionUID - Static variable in exception de.charite.compbio.jannovar.UncheckedJannovarException

set(int, NucleotideChange) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

Deprecated.

set(int, ProteinChange) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

Deprecated.

setAccession(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setAlleleCounts(HashMap<ExacPopulation, List<Integer>>) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setAlleleCounts(ArrayList<Integer>) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setAlleleFrequencies(ArrayList<Double>) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setAlleleFrequenciesG1K(ArrayList<Double>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setAlt(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setAlt(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setAlt(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setAssemblyConflict(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setAssemblySpecific(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setAttributes(ImmutableMap<String, String>) - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

setBegin(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setCDSRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setChromCount(int) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setChromCounts(HashMap<ExacPopulation, Integer>) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setChromType(ChromosomeType) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setClinicalDiagnosticAssay(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setCommon(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setCompatibleModes(TreeSet<ModeOfInheritance>) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

setContig(String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setContig(String) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setContig(String) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setContigAlelleNotVariant(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setCounter(int) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

setCurrentVC(VariantContext) - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

setDbSNPBuildID(int) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setEnd(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setFilter(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setFilter(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setFilter(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setFivePercentAll(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setFivePercentOne(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setFTPProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set FTP proxy URL

setG1kPhase1(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setG1kPhase3(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setGeneID(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setGeneInfos(ArrayList<DBSNPGeneInfo>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setGeneSymbol(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setGenomeRegions(ImmutableList<GenomeRegion>) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

setGenotypesAvailable(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setHasOMIMOrOMIA(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setHighDensityGenotyping(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setHTTPProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set HTTP proxy URL

setHTTPSProxy(URL) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set HTTPS proxy URL

setID(String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setID(String) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setID(String) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setIdentifierPrefix(String) - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

setInAcceptor(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInDonor(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInFivePrime(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInFivePrimeUTR(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInIntron(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInThreePrime(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setInThreePrimeUTR(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setIsXChromosomal(boolean) - Method in class de.charite.compbio.jannovar.pedigree.GenotypeListBuilder

Deprecated.

Set "is X chromosomal" flag of next build GenotypeCalls.

setLocusSpecificDatabase(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setMaxEnd(int) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setMicroattributionThirdParty(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setMultiMatchBehaviour(DBAnnotationOptions.MultipleMatchBehaviour) - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

setMutation(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setNameToRegion(ImmutableMap<String, GenomeRegion>) - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

setNonOverlappingAlleleSet(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setNonSynonymousFrameShift(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setNonSynonymousMissense(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setNonSynonymousNonsense(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setOldVariants(ArrayList<String>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setOtherVariant(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setPayload(Object) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setPos(int) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setPos(int) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setPos(int) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setPrecious(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setPrintProgressBars(boolean) - Method in class de.charite.compbio.jannovar.datasource.DatasourceOptions

Set whether to print progress bars or not

setPubMedCentral(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setRank(int) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setRankType(AnnotationLocation.RankType) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setRef(String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setRef(String) - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

setRef(String) - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

setReference(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setReportOverlapping(boolean) - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

setReportOverlappingAsMatching(boolean) - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

setReversed(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setRSID(int) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setRSPos(int) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setSampleToGenotype(TreeMap<String, Genotype>) - Method in class de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder

setSequence(String) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setSubmitterLinkOut(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setSynonymous(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setThirdPartyAnnotation(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setThreeDStructure(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setTranscript(TranscriptModel) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setTranscriptSupportLevel(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setTXLocation(TranscriptInterval) - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

setTXRegion(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

setValidated(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setValue(T) - Method in class de.charite.compbio.jannovar.impl.intervals.MutableInterval

setVariantAlleleOrigin(DBSNPVariantAlleleOrigin) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

setVariantProperty(DBSNPVariantProperty) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setVariantSuspectReasonCode(HashSet<DBSNPVariantSuspectReasonCode>) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setVariationClass(String) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setWeights(int) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

setWithdrawn(boolean) - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder

Sex - Enum in de.charite.compbio.jannovar.pedigree

Representation of an individual's sex.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.CDSPosition

Return shifted CDSPosition.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

Return shifted GenomePosition.

shifted(int) - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

Return shifted TranscriptPosition.

shiftInsertion(AminoAcidChange, String) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Shift insertion AminoAcidChange to the right in WT AA sequence.

shiftLeft() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

shiftRight() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

showAll - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether to report the annotations for all affected transcripts for each alternative allele

SingleAlleleNucleotideVariant - Class in de.charite.compbio.jannovar.hgvs.nts.variant

Nucleotide change with one allele only.

SingleAlleleNucleotideVariant(SequenceType, String, VariantConfiguration, Collection<? extends NucleotideChange>) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

Construct SingleAlleleNucleotideVariant

SingleAlleleNucleotideVariant(SequenceType, String, String, int, NucleotideChangeAllele) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

Construct SingleAlleleNucleotideVariant

SingleAlleleNucleotideVariant(SequenceType, String, NucleotideChangeAllele) - Constructor for class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

Construct SingleAlleleNucleotideVariant

SingleAlleleProteinVariant - Class in de.charite.compbio.jannovar.hgvs.protein.variant

Protein change with one allele only.

SingleAlleleProteinVariant(String, VariantConfiguration, Collection<? extends ProteinChange>) - Constructor for class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

Construct SingleAlleleProteinVariant

singleChangeAllele(NucleotideChange) - Static method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

singleChangeAllele(ProteinChange) - Static method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

size() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

size() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

size() - Method in class de.charite.compbio.jannovar.impl.intervals.IntervalArray

SNVAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Builds Annotation objects for the SNV GenomeVariants in the given TranscriptModel

start() - Method in class de.charite.compbio.jannovar.progress.ProgressReporter

Strand - Enum in de.charite.compbio.jannovar.reference

Representation for forward/backward strand.

StringUtil - Class in de.charite.compbio.jannovar.impl.util

StringUtil() - Constructor for class de.charite.compbio.jannovar.impl.util.StringUtil

StructuralVariantAnnotationBuilder - Class in de.charite.compbio.jannovar.annotation.builders

Class providing static functions for creating Annotation objects for SVs.

StructuralVariantAnnotationBuilder(TranscriptModel, GenomeVariant) - Constructor for class de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder

Initialize the builder for the structural variant GenomeVariant in the given TranscriptModel.

subList(int, int) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

subList(int, int) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

subsetOfMembers(Collection<String>) - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

Obtain subset of members in a pedigree or change order.

T

TO_LEGACY_NAME - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Function for converting from VariantEffect to legacy term.

TO_SO_TERM - Static variable in enum de.charite.compbio.jannovar.annotation.VariantEffect

Function for converting from VariantEffect to SO term String.

toArray() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

toArray(T[]) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

toArray() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

toArray(T[]) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

toDisease(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Parse String into a Disease value.

toDisplayString() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

A string representing the variant type (e.g., missense_variant, stop_gained,...)

toHGVSChunk() - Method in class de.charite.compbio.jannovar.annotation.AnnotationLocation

toHGVSSeparator() - Method in enum de.charite.compbio.jannovar.hgvs.VariantConfiguration

toHGVSString() - Method in interface de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

toHGVSString(AminoAcidCode) - Method in interface de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

toHGVSString(boolean) - Method in enum de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChangeType

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

toHGVSString(boolean) - Method in enum de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChangeType

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

toHGVSString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

toHGVSString(AminoAcidCode) - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

toInt() - Method in enum de.charite.compbio.jannovar.pedigree.Disease

toInt() - Method in enum de.charite.compbio.jannovar.pedigree.Sex

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyChange

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

toLegacyString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

Return human readable legacy HGVS notation

toLong(String) - Method in class de.charite.compbio.jannovar.hgvs.Translator

toLong(char) - Method in class de.charite.compbio.jannovar.hgvs.Translator

toLong(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

toLong(char) - Method in class de.charite.compbio.jannovar.impl.util.Translator

toSequenceOntologyID() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Return the sequence ontology accession number for the variant class if available, otherwise return the name.

toSequenceOntologyTerm() - Method in enum de.charite.compbio.jannovar.annotation.OldVariantType

A Sequence Ontology (SO) term string representing the variant type (e.g., missense_variant, stop_gained,...)

toSex(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Parse String into a Sex value.

toString() - Method in class de.charite.compbio.jannovar.annotation.Annotation

toString() - Method in class de.charite.compbio.jannovar.annotation.VariantAnnotations

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution

toString() - Method in class de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideRange

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

toString() - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.ProteinRange

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

toString() - Method in class de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant

toString() - Method in class de.charite.compbio.jannovar.impl.intervals.Interval

toString() - Method in class de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

toString() - Method in class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

toString() - Method in class de.charite.compbio.jannovar.mendel.Genotype

toString() - Method in class de.charite.compbio.jannovar.mendel.GenotypeCalls

toString() - Method in class de.charite.compbio.jannovar.pedigree.GenotypeList

Deprecated.

toString() - Method in class de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList

toString() - Method in class de.charite.compbio.jannovar.pedigree.Pedigree

toString() - Method in class de.charite.compbio.jannovar.pedigree.PedPerson

toString() - Method in class de.charite.compbio.jannovar.pedigree.Person

toString() - Method in class de.charite.compbio.jannovar.progress.GenomeRegion

toString() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

toString() - Method in class de.charite.compbio.jannovar.reference.AminoAcidChange

toString() - Method in class de.charite.compbio.jannovar.reference.CDSInterval

toString() - Method in class de.charite.compbio.jannovar.reference.CDSPosition

toString() - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

toString() - Method in class de.charite.compbio.jannovar.reference.GenomePosition

toString() - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

toString() - Method in enum de.charite.compbio.jannovar.reference.Strand

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptInterval

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

toString() - Method in class de.charite.compbio.jannovar.reference.TranscriptPosition

toString() - Method in class de.charite.compbio.jannovar.vardbs.base.AnnotatingRecord

toString() - Method in class de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions

toString() - Method in class de.charite.compbio.jannovar.vardbs.base.GenotypeMatch

toString() - Method in class de.charite.compbio.jannovar.vardbs.base.VariantDescription

toString() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo

toString() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo

toString() - Method in class de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord

toString() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecord

toString() - Method in class de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder

toString() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

toString() - Method in class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

totalLength() - Method in class de.charite.compbio.jannovar.progress.GenomeRegionList

toVCFAnnoString(String, boolean) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Return the standardized VCF variant string for the given ALT allele.

toVCFAnnoString(String) - Method in class de.charite.compbio.jannovar.annotation.Annotation

Forward to toVCFAnnoString(alt, true).

transcript - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.transcript of next build AnnotationLocation.

TranscriptInterval - Class in de.charite.compbio.jannovar.reference

Interval on a transcript.

TranscriptInterval(TranscriptModel, int, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptInterval

construct transcript interval with one-based coordinate system

TranscriptInterval(TranscriptModel, int, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptInterval

construct transcript interval with selected coordinate system

TranscriptIntervalEndExtractor - Class in de.charite.compbio.jannovar.reference

Extraction of interval end points for TranscriptModel.

TranscriptIntervalEndExtractor() - Constructor for class de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor

transcriptLength() - Method in class de.charite.compbio.jannovar.reference.TranscriptModel

TranscriptModel - Class in de.charite.compbio.jannovar.reference

The information representing a transcript model.

TranscriptModel(String, String, GenomeInterval, GenomeInterval, ImmutableList<GenomeInterval>, String, String, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel

Initialize the TranscriptInfo object from the given parameters.

TranscriptModel(String, String, GenomeInterval, GenomeInterval, ImmutableList<GenomeInterval>, String, String, int, Map<String, String>) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModel

Initialize the TranscriptInfo object from the given parameters.

TranscriptModelBuilder - Class in de.charite.compbio.jannovar.reference

Class for building immutable TranscriptModel objects field-by-field.

TranscriptModelBuilder() - Constructor for class de.charite.compbio.jannovar.reference.TranscriptModelBuilder

TranscriptParseException - Exception in de.charite.compbio.jannovar.impl.parse

Exception that occurs during parsing of transcript database files.

TranscriptParseException() - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParseException(String) - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParseException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.impl.parse.TranscriptParseException

TranscriptParser - Interface in de.charite.compbio.jannovar.impl.parse

General interface for transcript parsers.

TranscriptPosition - Class in de.charite.compbio.jannovar.reference

Position on a transcript.

TranscriptPosition(TranscriptModel, int) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptPosition

construct transcript position with one-based coordinate system

TranscriptPosition(TranscriptModel, int, PositionType) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptPosition

construct transcript position with selected coordinate system

TranscriptProjectionDecorator - Class in de.charite.compbio.jannovar.reference

Wraps a TranscriptModel object and allow the coordinate conversion.

TranscriptProjectionDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Initialize the object with the given TranscriptModel

TranscriptSequenceChangeHelper - Class in de.charite.compbio.jannovar.reference

Helper class for getting updated transcript sequence for deletions and block substitutions.

TranscriptSequenceChangeHelper(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper

Construct helper with the given TranscriptModel

TranscriptSequenceDecorator - Class in de.charite.compbio.jannovar.reference

Decorator for TranscriptModel that helps with operations on its sequence

TranscriptSequenceDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator

TranscriptSequenceOntologyDecorator - Class in de.charite.compbio.jannovar.reference

Functionality for finding out about certain points/regions of TranscriptModel using genomic positions.

TranscriptSequenceOntologyDecorator(TranscriptModel) - Constructor for class de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator

Initialize the object with the given TranscriptModel.

TranscriptSupportLevels - Interface in de.charite.compbio.jannovar.reference

Container for constants of transcript support levels.

TranscriptSupportLevelsSetterFromLengths - Class in de.charite.compbio.jannovar.impl.parse

Set the transcript support level from transcript lengths.

TranscriptSupportLevelsSetterFromLengths() - Constructor for class de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths

transcriptToGenomePos(TranscriptPosition) - Method in class de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

Coordinate conversion from transcript to genome position.

translateDNA(String) - Method in class de.charite.compbio.jannovar.hgvs.Translator

Translates a DNA sequence.

translateDNA(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

Translates a DNA sequence.

translateDNA3(String) - Method in class de.charite.compbio.jannovar.hgvs.Translator

translateDNA3(String) - Method in class de.charite.compbio.jannovar.impl.util.Translator

translateNucleotidePointLocation(TranscriptModel, NucleotidePointLocation, SequenceType) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter

Convert NucleotidePointLocation on a TranscriptModel to a GenomePosition

translateNucleotideRange(TranscriptModel, NucleotideRange, SequenceType) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter

Convert NucleotideRange on a TranscriptModel to a GenomePosition

translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator

Shortcut to NucleotideChangeToGenomeVariantTranslator.translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) with using true for the second parameter.

translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) - Method in class de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator

Translate single-change SingleAlleleNucleotideVariant into a GenomeVariant

Translator - Class in de.charite.compbio.jannovar.hgvs

This singleton class helps to translate DNA sequences.

Translator - Class in de.charite.compbio.jannovar.impl.util

This singleton class helps to translate DNA sequences.

truncateAltAfterStopCodon(AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Search for stop codon in change.alt and truncate afterwards.

truncateBothSides(AminoAcidChange) - Static method in class de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer

Truncate AminoAcidChange from both sides for matching ref/alt prefixes/suffixes.

TSL1 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

All splice junctions of the transcript are supported by at least one non-suspect mRNA.

TSL2 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The best supporting mRNA is flagged as suspect or the support is from multiple ESTs.

TSL3 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The only support is from a single EST.

TSL4 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

The best supporting EST is flagged as suspect.

TSL5 - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

No single transcript supports the model structure.

txLocation - Variable in class de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder

AnnotationLocation.txLocation of next build AnnotationLocation.

U

UCSC_CANONICAL - Static variable in interface de.charite.compbio.jannovar.reference.TranscriptSupportLevels

Annotated as canonical transcript by UCSC (used in absence of TSL).

UCSCParser - Class in de.charite.compbio.jannovar.impl.parse.ucsc

Parser for the UCCSC knownGene and related files.

UCSCParser(ReferenceDictionary, String, Profile.Section) - Constructor for class de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser

UK10KAnnotationDriver - Class in de.charite.compbio.jannovar.vardbs.uk10k

Annotation driver class for annotations using UK10K data

UK10KAnnotationDriver(String, String, DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.uk10k.UK10KAnnotationDriver

UK10KRecord - Class in de.charite.compbio.jannovar.vardbs.uk10k

UK10KRecord(String, int, String, String, List<String>, List<String>, int, List<Integer>, List<Double>) - Constructor for class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord

UK10KRecordBuilder - Class in de.charite.compbio.jannovar.vardbs.uk10k

UK10KRecordBuilder() - Constructor for class de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder

UK10KVCFHeaderExtender - Class in de.charite.compbio.jannovar.vardbs.uk10k

Helper class for extending VCFHeaders for UK10K annotations.

UK10KVCFHeaderExtender(DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.uk10k.UK10KVCFHeaderExtender

UncheckedJannovarException - Exception in de.charite.compbio.jannovar

Base class for unchecked exceptions in Jannovar

UncheckedJannovarException() - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

UncheckedJannovarException(String) - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

UncheckedJannovarException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.UncheckedJannovarException

union(GenomeInterval) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

useThreeLetterAminoAcidCode - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether to use 3 letter amino acid code instead of 1 letter

V

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationMessage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.PutativeImpact

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.AminoAcidCode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.legacy.LegacyLocationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChangeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChangeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.SequenceType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.hgvs.VariantConfiguration

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.htsjdk.InfoFields

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.JannovarOptions.Command

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.mendel.ChromosomeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Genotype

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.GenomeVariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.PositionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.reference.Strand

Returns the enum constant of this type with the specified name.

valueOf(char) - Method in enum de.charite.compbio.jannovar.reference.Strand

valueOf(String) - Static method in enum de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions.MultipleMatchBehaviour

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantAlleleOrigin

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantSuspectReasonCode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.charite.compbio.jannovar.vardbs.exac.ExacPopulation

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.AnnotationMessage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.OldVariantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.PutativeImpact

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.annotation.VariantEffect

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.AminoAcidCode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.legacy.LegacyLocationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChangeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChangeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.SequenceType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.hgvs.VariantConfiguration

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.htsjdk.InfoFields

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.JannovarOptions.Command

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.mendel.ChromosomeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.mendel.ModeOfInheritance

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Disease

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Genotype

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.pedigree.Sex

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.GenomeVariantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.PositionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.reference.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions.MultipleMatchBehaviour

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantAlleleOrigin

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantSuspectReasonCode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.charite.compbio.jannovar.vardbs.exac.ExacPopulation

Returns an array containing the constants of this enum type, in the order they are declared.

VariantAnnotations - Class in de.charite.compbio.jannovar.annotation

A list of priority-sorted Annotation objects.

VariantAnnotations(GenomeVariant, Collection<Annotation>) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotations

Construct ImmutableAnnotationList from a Collection of Annotation objects.

VariantAnnotationsContentDecorator - Class in de.charite.compbio.jannovar.annotation

Decorator for VariantAnnotations that allows queries on the content.

VariantAnnotationsContentDecorator(VariantAnnotations) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator

Initialize the decorator.

VariantAnnotationsTextGenerator - Class in de.charite.compbio.jannovar.annotation

Generate annotation text (effect and HGVS description) from VariantAnnotations object.

VariantAnnotationsTextGenerator(VariantAnnotations, int, int) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator

Initialize the decorator.

VariantAnnotator - Class in de.charite.compbio.jannovar.annotation

Main driver class for annotating variants.

VariantAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>, AnnotationBuilderOptions) - Constructor for class de.charite.compbio.jannovar.annotation.VariantAnnotator

Construct new VariantAnnotator, given a chromosome map.

VariantConfiguration - Enum in de.charite.compbio.jannovar.hgvs

Variant configuration of changes in the same gene.

VariantContextAnnotator - Class in de.charite.compbio.jannovar.htsjdk

Helper class for generating VariantAnnotations objects from VariantContexts.

VariantContextAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Construct annotator with default options.

VariantContextAnnotator(ReferenceDictionary, ImmutableMap<Integer, Chromosome>, VariantContextAnnotator.Options) - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

Construct Annotator.

VariantContextAnnotator.Options - Class in de.charite.compbio.jannovar.htsjdk

Options class for VariantContextAnnotator

VariantContextCompatibilityCheckerAutosomalDominant - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and autosomal dominant mode of inheritance.

VariantContextCompatibilityCheckerAutosomalDominant(Pedigree, List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant

Initialize compatibility checker for autosomal dominant and perform some sanity checks.

VariantContextCompatibilityCheckerAutosomalDominant(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant

Initialize compatibility checker for AutosomaöDominant and perform some sanity checks.

VariantContextCompatibilityCheckerAutosomalRecessive - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and autosomal recessive mode of inheritance.

VariantContextCompatibilityCheckerAutosomalRecessive(Pedigree, List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive

Initialize compatibility checker for Autosomal recessive and perform some sanity checks.

VariantContextCompatibilityCheckerAutosomalRecessive(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive

Initialize compatibility checker for autosomal recessive and perform some sanity checks.

VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and autosomal recessive compound het mode of inheritance.

VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet

Initialize compatibility checker for autosomal recessive compund het and perform some sanity checks.

VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and autosomal recessive homozygous mode of inheritance.

VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

Initialize compatibility checker for autosomal recessive homozygout and perform some sanity checks.

VariantContextCompatibilityCheckerXDominant - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and X dominant mode of inheritance.

VariantContextCompatibilityCheckerXDominant(Pedigree, List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

Initialize compatibility checker for X dominant and perform some sanity checks.

VariantContextCompatibilityCheckerXDominant(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

Initialize compatibility checker for X dominant t and perform some sanity checks.

VariantContextCompatibilityCheckerXRecessive - Class in de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and X recessive mode of inheritance.

VariantContextCompatibilityCheckerXRecessive(Pedigree, InheritanceVariantContextList) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive

Initialize compatibility checker for X recessive and perform some sanity checks.

VariantContextCompatibilityCheckerXRecessive(Pedigree, List<VariantContext>) - Constructor for class de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive

Initialize compatibility checker for X recessive and perform some sanity checks.

VariantContextCounter - Class in de.charite.compbio.jannovar.mendel.filter

A VariantContext with an integer counter and set of compatible modes

VariantContextCounter(VariantContext) - Constructor for class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

VariantContextCounter(VariantContext, int) - Constructor for class de.charite.compbio.jannovar.mendel.filter.VariantContextCounter

VariantContextFilterException - Exception in de.charite.compbio.jannovar.mendel.filter

Thrown on problems during the filtration.

VariantContextFilterException(String) - Constructor for exception de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException

VariantContextFilterException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException

VariantContextMendelianAnnotator - Class in de.charite.compbio.jannovar.mendel.bridge

Helper class for annotating one VariantContext or a Collection thereof for compatibility with Mendelian inheritance

VariantContextMendelianAnnotator(Pedigree) - Constructor for class de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator

VariantContextProcessor - Interface in de.charite.compbio.jannovar.mendel.filter

Step in a VariantContext processing pipeline, designed as a sink

VariantContextToRecordConverter<RecordType> - Interface in de.charite.compbio.jannovar.vardbs.base

Conversion of VariantContext objects to record objects.

VariantContextWriterConstructionHelper - Class in de.charite.compbio.jannovar.htsjdk

Helper for creating a VariantContextWriter from a OutputStream.

VariantContextWriterConstructionHelper() - Constructor for class de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

VariantDescription - Interface in de.charite.compbio.jannovar.reference

Minimal description of a variant as triple (position, ref, alt).

VariantDescription - Class in de.charite.compbio.jannovar.vardbs.base

Simple variant description, for use with variant normalization

VariantDescription(String, int, String, String) - Constructor for class de.charite.compbio.jannovar.vardbs.base.VariantDescription

VariantEffect - Enum in de.charite.compbio.jannovar.annotation

These codes reflect the possible types of variants that we call for an exome.

VariantNormalizer - Class in de.charite.compbio.jannovar.vardbs.base

Helper class for normalizing two variants This is necessary for indel realignment.

VariantNormalizer(String) - Constructor for class de.charite.compbio.jannovar.vardbs.base.VariantNormalizer

Construct new variant normalizer object

VCF_ANN_DESCRIPTION_STRING - Static variable in class de.charite.compbio.jannovar.annotation.Annotation

The DESCRIPTION string to use in the VCF header for VCFVariantAnnotation objects

vcfFilePaths - Variable in class de.charite.compbio.jannovar.JannovarOptions

path to a VCF file to be annotated

VCFHeaderExtender - Class in de.charite.compbio.jannovar.vardbs.base

Extend VCFHeader object with headers for a given database

VCFHeaderExtender(DBAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.vardbs.base.VCFHeaderExtender

verbosity - Variable in class de.charite.compbio.jannovar.JannovarOptions

verbosity level

W

withMorePadding(int) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

withMorePadding(int, int) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability

withOnlyPredicted(boolean) - Method in class de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomeInterval

convert into GenomeInterval of the given strand

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomePosition

convert into GenomePosition of the given strand

withStrand(Strand) - Method in class de.charite.compbio.jannovar.reference.GenomeVariant

write(PedFileContents) - Method in class de.charite.compbio.jannovar.pedigree.PedFileWriter

Write out the PedFileContents object to the output.

write(PedFileContents, OutputStream) - Static method in class de.charite.compbio.jannovar.pedigree.PedFileWriter

Static method for writing a PedFileContents file to a OutputStream.

writeJannovarInfoFields - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether or not to write out the old Jannovar annotation VCF tags

writeVCFAnnotationStandardInfoFields - Variable in class de.charite.compbio.jannovar.JannovarOptions

whether or not to write out the VCF annotation standard fields

X

XD - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

Constant for X dominant

XR - Static variable in class de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender

Constant for X recessive

A B C D E F G H I J K L M N O P R S T U V W X