A C E F G H I O P R S T U V W Z

A

A - Static variable in class org.molgenis.genotype.Allele

add(String, String) - Method in class org.molgenis.vcf.meta.VcfMeta

addAltMeta(VcfMetaAlt) - Method in class org.molgenis.vcf.meta.VcfMeta

addContigMeta(VcfMetaContig) - Method in class org.molgenis.vcf.meta.VcfMeta

addFilterMeta(VcfMetaFilter) - Method in class org.molgenis.vcf.meta.VcfMeta

addFormatMeta(VcfMetaFormat) - Method in class org.molgenis.vcf.meta.VcfMeta

addInfoMeta(VcfMetaInfo) - Method in class org.molgenis.vcf.meta.VcfMeta

addPedigreeMeta(VcfMetaPedigree) - Method in class org.molgenis.vcf.meta.VcfMeta

addSampleMeta(VcfMetaSample) - Method in class org.molgenis.vcf.meta.VcfMeta

Allele - Class in org.molgenis.genotype

C

C - Static variable in class org.molgenis.genotype.Allele

close() - Method in class org.molgenis.vcf.v4_2.Vcf42Writer

close() - Method in class org.molgenis.vcf.VcfReader

COL_ALT_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_CHROM_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_FILTER_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_FORMAT_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_ID_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_INFO_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_POS_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_QUAL_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

COL_REF_IDX - Static variable in class org.molgenis.vcf.meta.VcfMeta

compareTo(Allele) - Method in class org.molgenis.genotype.Allele

COMPLEMENTAL_NUCLEOTIDES - Static variable in class org.molgenis.genotype.util.Utils

create(String) - Static method in class org.molgenis.genotype.Allele

create(char) - Static method in class org.molgenis.genotype.Allele

create(File, VcfMeta) - Method in class org.molgenis.vcf.VcfWriterFactory

Returns a Vcf42Writer to write gzipped or uncompressed content to file based on the file name extension.

create(File, VcfMeta, VcfWriterFactory.Format) - Method in class org.molgenis.vcf.VcfWriterFactory

create(File, VcfMeta, VcfWriterFactory.Format, VcfWriterFactory.Version) - Method in class org.molgenis.vcf.VcfWriterFactory

create(OutputStream, VcfMeta) - Method in class org.molgenis.vcf.VcfWriterFactory

create(OutputStream, VcfMeta, VcfWriterFactory.Format) - Method in class org.molgenis.vcf.VcfWriterFactory

create(OutputStream, VcfMeta, VcfWriterFactory.Format, VcfWriterFactory.Version) - Method in class org.molgenis.vcf.VcfWriterFactory

createClone() - Method in class org.molgenis.vcf.VcfRecord

createClone() - Method in class org.molgenis.vcf.VcfSample

E

equals(Object) - Method in class org.molgenis.genotype.Allele

equals(Object) - Method in class org.molgenis.vcf.meta.VcfMetaEntry

equals(Object) - Method in class org.molgenis.vcf.VcfInfo

equals(Object) - Method in class org.molgenis.vcf.VcfRecord

F

from(String) - Static method in enum org.molgenis.vcf.meta.VcfMetaFormat.Type

from(String) - Static method in enum org.molgenis.vcf.meta.VcfMetaInfo.Type

G

G - Static variable in class org.molgenis.genotype.Allele

GenotypeDataException - Exception in org.molgenis.genotype

GenotypeDataException() - Constructor for exception org.molgenis.genotype.GenotypeDataException

GenotypeDataException(String) - Constructor for exception org.molgenis.genotype.GenotypeDataException

GenotypeDataException(Throwable) - Constructor for exception org.molgenis.genotype.GenotypeDataException

GenotypeDataException(String, Throwable) - Constructor for exception org.molgenis.genotype.GenotypeDataException

get(String) - Method in class org.molgenis.vcf.meta.VcfMeta

get(String) - Method in class org.molgenis.vcf.meta.VcfMetaEntry

getAlleleAsSnp() - Method in class org.molgenis.genotype.Allele

getAlleleAsString() - Method in class org.molgenis.genotype.Allele

getAlleles() - Method in class org.molgenis.vcf.VcfSample

getAlt(VcfRecord, int) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAlt(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAltAlleleIndex(VcfRecord, String) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAltAlleleOrderedDoubleField(VcfRecord, String) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAlternateAlleles() - Method in class org.molgenis.vcf.VcfRecord

getAltIndex(VcfRecord, String) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAltMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getAltMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getAlts(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAltsAsStringArray(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getAltString(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getChromosome() - Method in class org.molgenis.vcf.VcfRecord

getChrPosRefAlt(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getColNames() - Method in class org.molgenis.vcf.meta.VcfMeta

getComplement() - Method in class org.molgenis.genotype.Allele

getComplementNucleotide(char) - Static method in class org.molgenis.genotype.util.Utils

getContigMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getContigMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getData(int) - Method in class org.molgenis.vcf.VcfSample

getDescription() - Method in class org.molgenis.vcf.meta.VcfMetaAlt

getDescription() - Method in class org.molgenis.vcf.meta.VcfMetaFilter

getDescription() - Method in class org.molgenis.vcf.meta.VcfMetaFormat

getDescription() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getFileFormat() - Method in class org.molgenis.vcf.meta.VcfMeta

getFilterMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getFilterMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getFilterStatus() - Method in class org.molgenis.vcf.VcfRecord

getFormat() - Method in class org.molgenis.vcf.VcfRecord

getFormatIndex(String) - Method in class org.molgenis.vcf.VcfRecord

getFormatMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getFormatMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getId() - Method in class org.molgenis.vcf.meta.VcfMetaAlt

getId() - Method in class org.molgenis.vcf.meta.VcfMetaContig

getId() - Method in class org.molgenis.vcf.meta.VcfMetaFilter

getId() - Method in class org.molgenis.vcf.meta.VcfMetaFormat

getId() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getId() - Method in class org.molgenis.vcf.meta.VcfMetaSample

getId(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getIdentifiers() - Method in class org.molgenis.vcf.VcfRecord

getInfoMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getInfoMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getInformation() - Method in class org.molgenis.vcf.VcfRecord

getInformation(String, VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getKey() - Method in class org.molgenis.vcf.VcfInfo

getLength() - Method in class org.molgenis.vcf.meta.VcfMetaContig

getMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getName() - Method in class org.molgenis.vcf.meta.VcfMetaAlt

getName() - Method in class org.molgenis.vcf.meta.VcfMetaContig

getName() - Method in class org.molgenis.vcf.meta.VcfMetaEntry

getName() - Method in class org.molgenis.vcf.meta.VcfMetaFilter

getName() - Method in class org.molgenis.vcf.meta.VcfMetaFormat

getName() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getName() - Method in class org.molgenis.vcf.meta.VcfMetaPedigree

getName() - Method in class org.molgenis.vcf.meta.VcfMetaSample

getNrSamples() - Method in class org.molgenis.vcf.VcfRecord

getNumber() - Method in class org.molgenis.vcf.meta.VcfMetaFormat

getNumber() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getPedigreeMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getPhasings() - Method in class org.molgenis.vcf.VcfSample

getPosition() - Method in class org.molgenis.vcf.VcfRecord

getProperties() - Method in class org.molgenis.vcf.meta.VcfMetaContig

getProperties() - Method in class org.molgenis.vcf.meta.VcfMetaEntry

getProperties() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getQuality() - Method in class org.molgenis.vcf.VcfRecord

getRef(VcfRecord) - Static method in class org.molgenis.vcf.VcfRecordUtils

getReferenceAllele() - Method in class org.molgenis.vcf.VcfRecord

getSampleFieldValue(VcfRecord, VcfSample, String) - Static method in class org.molgenis.vcf.VcfRecordUtils

getSampleMeta() - Method in class org.molgenis.vcf.meta.VcfMeta

getSampleMeta(String) - Method in class org.molgenis.vcf.meta.VcfMeta

getSampleName(int) - Method in class org.molgenis.vcf.meta.VcfMeta

getSampleNames() - Method in class org.molgenis.vcf.meta.VcfMeta

getSamples() - Method in class org.molgenis.vcf.VcfRecord

getSource() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getTokens() - Method in class org.molgenis.vcf.VcfRecord

getTokens() - Method in class org.molgenis.vcf.VcfSample

getType() - Method in class org.molgenis.vcf.meta.VcfMetaFormat

getType() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

getVal() - Method in class org.molgenis.vcf.VcfInfo

getValRaw() - Method in class org.molgenis.vcf.VcfInfo

getVcfMeta() - Method in class org.molgenis.vcf.VcfReader

getVcfMeta() - Method in class org.molgenis.vcf.VcfRecord

getVersion() - Method in class org.molgenis.vcf.meta.VcfMetaInfo

H

hashCode() - Method in class org.molgenis.genotype.Allele

hashCode() - Method in class org.molgenis.vcf.meta.VcfMetaEntry

hashCode() - Method in class org.molgenis.vcf.VcfInfo

hashCode() - Method in class org.molgenis.vcf.VcfRecord

I

isSnpAllele() - Method in class org.molgenis.genotype.Allele

iterator() - Method in class org.molgenis.vcf.VcfReader

iterator() - Method in class org.molgenis.vcf.VcfRecordReader

O

org.molgenis.genotype - package org.molgenis.genotype

org.molgenis.genotype.util - package org.molgenis.genotype.util

org.molgenis.vcf - package org.molgenis.vcf

org.molgenis.vcf.meta - package org.molgenis.vcf.meta

org.molgenis.vcf.v4_2 - package org.molgenis.vcf.v4_2

P

parse() - Method in class org.molgenis.vcf.meta.VcfMetaParser

properties - Variable in class org.molgenis.vcf.meta.VcfMetaEntry

R

reset(String, String) - Method in class org.molgenis.vcf.VcfInfo

reset(String[]) - Method in class org.molgenis.vcf.VcfRecord

reset(String[]) - Method in class org.molgenis.vcf.VcfSample

S

setColNames(String[]) - Method in class org.molgenis.vcf.meta.VcfMeta

setVcfMetaSamples(Map<String, VcfMetaSample>) - Method in class org.molgenis.vcf.meta.VcfMeta

T

T - Static variable in class org.molgenis.genotype.Allele

toString() - Method in class org.molgenis.genotype.Allele

toString() - Method in class org.molgenis.vcf.meta.VcfMeta

toString() - Method in class org.molgenis.vcf.meta.VcfMetaEntry

toString() - Method in enum org.molgenis.vcf.meta.VcfMetaFormat.Type

toString() - Method in enum org.molgenis.vcf.meta.VcfMetaInfo.Type

toString() - Method in class org.molgenis.vcf.VcfRecord

U

Utils - Class in org.molgenis.genotype.util

General Uilities

Utils() - Constructor for class org.molgenis.genotype.util.Utils

V

valueOf(String) - Static method in enum org.molgenis.vcf.meta.VcfMetaFormat.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.molgenis.vcf.meta.VcfMetaInfo.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.molgenis.vcf.VcfWriterFactory.Format

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.molgenis.vcf.VcfWriterFactory.Version

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.vcf.meta.VcfMetaFormat.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.molgenis.vcf.meta.VcfMetaInfo.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.molgenis.vcf.VcfWriterFactory.Format

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.molgenis.vcf.VcfWriterFactory.Version

Returns an array containing the constants of this enum type, in the order they are declared.

Vcf42Writer - Class in org.molgenis.vcf.v4_2

VCF v4.2 writer

Vcf42Writer(OutputStream, VcfMeta) - Constructor for class org.molgenis.vcf.v4_2.Vcf42Writer

VcfInfo - Class in org.molgenis.vcf

VcfInfo(VcfMeta) - Constructor for class org.molgenis.vcf.VcfInfo

VcfInfo(VcfMeta, String, String) - Constructor for class org.molgenis.vcf.VcfInfo

VcfMeta - Class in org.molgenis.vcf.meta

VcfMeta() - Constructor for class org.molgenis.vcf.meta.VcfMeta

VcfMetaAlt - Class in org.molgenis.vcf.meta

VcfMetaAlt(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaAlt

VcfMetaContig - Class in org.molgenis.vcf.meta

VcfMetaContig(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaContig

VcfMetaEntry - Class in org.molgenis.vcf.meta

VcfMetaEntry(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaEntry

VcfMetaFilter - Class in org.molgenis.vcf.meta

VcfMetaFilter(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaFilter

VcfMetaFormat - Class in org.molgenis.vcf.meta

VcfMetaFormat(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaFormat

VcfMetaFormat.Type - Enum in org.molgenis.vcf.meta

VcfMetaInfo - Class in org.molgenis.vcf.meta

VcfMetaInfo(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaInfo

VcfMetaInfo.Type - Enum in org.molgenis.vcf.meta

VcfMetaParser - Class in org.molgenis.vcf.meta

VcfMetaParser(Reader) - Constructor for class org.molgenis.vcf.meta.VcfMetaParser

VcfMetaParser(BlockCompressedInputStream) - Constructor for class org.molgenis.vcf.meta.VcfMetaParser

VcfMetaPedigree - Class in org.molgenis.vcf.meta

VcfMetaPedigree(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaPedigree

VcfMetaSample - Class in org.molgenis.vcf.meta

VcfMetaSample(Map<String, String>) - Constructor for class org.molgenis.vcf.meta.VcfMetaSample

VcfReader - Class in org.molgenis.vcf

A high-performance VCF reader based on the the Variant Call Format (VCF) Version 4.2 Specification

VcfReader(Reader) - Constructor for class org.molgenis.vcf.VcfReader

VcfReader(BlockCompressedInputStream) - Constructor for class org.molgenis.vcf.VcfReader

VcfRecord - Class in org.molgenis.vcf

VcfRecord(VcfMeta) - Constructor for class org.molgenis.vcf.VcfRecord

VcfRecord(VcfMeta, String[]) - Constructor for class org.molgenis.vcf.VcfRecord

VcfRecordReader - Class in org.molgenis.vcf

VcfRecordReader(Reader, VcfMeta) - Constructor for class org.molgenis.vcf.VcfRecordReader

VcfRecordReader(BlockCompressedInputStream, VcfMeta) - Constructor for class org.molgenis.vcf.VcfRecordReader

VcfRecordUtils - Class in org.molgenis.vcf

VcfSample - Class in org.molgenis.vcf

VcfSample(VcfRecord) - Constructor for class org.molgenis.vcf.VcfSample

VcfSample(VcfRecord, String[]) - Constructor for class org.molgenis.vcf.VcfSample

VcfWriter - Interface in org.molgenis.vcf

VcfWriterFactory - Class in org.molgenis.vcf

VcfWriterFactory() - Constructor for class org.molgenis.vcf.VcfWriterFactory

VcfWriterFactory.Format - Enum in org.molgenis.vcf

VcfWriterFactory.Version - Enum in org.molgenis.vcf

W

write(VcfRecord) - Method in class org.molgenis.vcf.v4_2.Vcf42Writer

write(VcfRecord) - Method in interface org.molgenis.vcf.VcfWriter

Z

ZERO - Static variable in class org.molgenis.genotype.Allele

A C E F G H I O P R S T U V W Z