htsjdk.variant.vcf

Class VCFConstants

java.lang.Object

htsjdk.variant.vcf.VCFConstants

public final class VCFConstants
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALLELE_COUNT_KEY
static java.lang.String	ALLELE_FREQUENCY_KEY
static java.lang.String	ALLELE_NUMBER_KEY
static java.lang.String	ALT_HEADER_START
static java.lang.String	ANCESTRAL_ALLELE_KEY
static java.lang.String	CIGAR_KEY
static java.lang.String	CONTIG_HEADER_KEY
static java.lang.String	CONTIG_HEADER_START
static java.lang.String	DBSNP_KEY
static char	DELETION_ALLELE_v3
static java.lang.String	DEPTH_KEY
static java.lang.String	EMPTY_ALLELE
static java.lang.String	EMPTY_ALTERNATE_ALLELE_FIELD
static java.lang.String	EMPTY_GENOTYPE
static java.lang.String	EMPTY_ID_FIELD
static java.lang.String	EMPTY_INFO_FIELD
static java.lang.String	END_KEY
static java.lang.String	EXPECTED_ALLELE_COUNT_KEY
static java.lang.String	FIELD_SEPARATOR
static char	FIELD_SEPARATOR_CHAR
static java.lang.String	FILTER_CODE_SEPARATOR
static java.lang.String	FILTER_HEADER_START
static java.lang.String	FORMAT_FIELD_SEPARATOR
static java.lang.String	FORMAT_HEADER_START
static java.lang.String	GENOTYPE_ALLELE_DEPTHS
static java.lang.String	GENOTYPE_FIELD_SEPARATOR
static char	GENOTYPE_FIELD_SEPARATOR_CHAR
static java.lang.String	GENOTYPE_FILTER_KEY
static java.lang.String	GENOTYPE_KEY
static java.lang.String	GENOTYPE_LIKELIHOODS_KEY Deprecated.
static java.lang.String	GENOTYPE_PL_KEY
static java.lang.String	GENOTYPE_POSTERIORS_KEY
static java.lang.String	GENOTYPE_QUALITY_KEY
static java.lang.String	HAPLOTYPE_QUALITY_KEY
static java.lang.String	HAPMAP2_KEY
static java.lang.String	HAPMAP3_KEY
static java.lang.String	ID_FIELD_SEPARATOR
static java.lang.String	INFO_FIELD_ARRAY_SEPARATOR
static char	INFO_FIELD_ARRAY_SEPARATOR_CHAR
static java.lang.String	INFO_FIELD_SEPARATOR
static char	INFO_FIELD_SEPARATOR_CHAR
static java.lang.String	INFO_HEADER_START
static char	INSERTION_ALLELE_v3
static java.lang.String	MAPPING_QUALITY_ZERO_KEY
static int	MAX_GENOTYPE_QUAL
static java.lang.String	MISSING_DEPTH_v3
static java.lang.String	MISSING_GENOTYPE_QUALITY_v3
static java.lang.String	MISSING_HAPLOTYPE_QUALITY_v3
static java.lang.String	MISSING_QUALITY_v3
static java.lang.Double	MISSING_QUALITY_v3_DOUBLE
static java.lang.String	MISSING_VALUE_v4
static char	NO_CALL_ALLELE
static char	NULL_ALLELE
static java.lang.String	OLD_DEPTH_KEY
static java.lang.String	PASSES_FILTERS_v3
static java.lang.String	PASSES_FILTERS_v4
static java.lang.String	PER_ALLELE_COUNT
static java.lang.String	PER_ALTERNATE_COUNT
static java.lang.String	PER_GENOTYPE_COUNT
static java.lang.String	PHASE_QUALITY_KEY
static java.lang.String	PHASE_SET_KEY
static java.lang.String	PHASED
static java.lang.String	PHASED_SWITCH_PROB_v3
static java.lang.String	PHASING_TOKENS
static java.lang.String	RMS_BASE_QUALITY_KEY
static java.lang.String	RMS_MAPPING_QUALITY_KEY
static java.lang.String	SAMPLE_NUMBER_KEY
static java.lang.String	SOMATIC_KEY
static char	SPANNING_DELETION_ALLELE
static java.lang.String	STRAND_BIAS_KEY
static java.lang.String	SVTYPE INFO Type of structural variant
static java.lang.String	THOUSAND_GENOMES_KEY
static java.lang.String	UNBOUNDED_ENCODING_v3
static java.lang.String	UNBOUNDED_ENCODING_v4
static java.lang.String	UNFILTERED
static java.lang.String	UNPHASED
static java.lang.String	VALIDATED_KEY
static java.lang.Double	VCF_ENCODING_EPSILON
static java.util.Locale	VCF_LOCALE

Constructor Summary

Constructors

Constructor and Description
VCFConstants()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VCF_LOCALE

public static final java.util.Locale VCF_LOCALE

ANCESTRAL_ALLELE_KEY

public static final java.lang.String ANCESTRAL_ALLELE_KEY

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Constant Field Values

ALLELE_COUNT_KEY

public static final java.lang.String ALLELE_COUNT_KEY

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Constant Field Values

ALLELE_FREQUENCY_KEY

public static final java.lang.String ALLELE_FREQUENCY_KEY

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Constant Field Values

ALLELE_NUMBER_KEY

public static final java.lang.String ALLELE_NUMBER_KEY

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Constant Field Values

RMS_BASE_QUALITY_KEY

public static final java.lang.String RMS_BASE_QUALITY_KEY

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Constant Field Values

CIGAR_KEY

public static final java.lang.String CIGAR_KEY

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Constant Field Values

DBSNP_KEY

public static final java.lang.String DBSNP_KEY

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Constant Field Values

DEPTH_KEY

public static final java.lang.String DEPTH_KEY

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Constant Field Values

END_KEY

public static final java.lang.String END_KEY

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Constant Field Values

GENOTYPE_FILTER_KEY

public static final java.lang.String GENOTYPE_FILTER_KEY

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Constant Field Values

GENOTYPE_KEY

public static final java.lang.String GENOTYPE_KEY

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Constant Field Values

GENOTYPE_POSTERIORS_KEY

public static final java.lang.String GENOTYPE_POSTERIORS_KEY

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Constant Field Values

GENOTYPE_QUALITY_KEY

public static final java.lang.String GENOTYPE_QUALITY_KEY

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Constant Field Values

GENOTYPE_ALLELE_DEPTHS

public static final java.lang.String GENOTYPE_ALLELE_DEPTHS

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Constant Field Values

GENOTYPE_PL_KEY

public static final java.lang.String GENOTYPE_PL_KEY

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Constant Field Values

EXPECTED_ALLELE_COUNT_KEY

public static final java.lang.String EXPECTED_ALLELE_COUNT_KEY

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Constant Field Values

GENOTYPE_LIKELIHOODS_KEY

@Deprecated
public static final java.lang.String GENOTYPE_LIKELIHOODS_KEY

Deprecated.

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Constant Field Values

HAPMAP2_KEY

public static final java.lang.String HAPMAP2_KEY

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Constant Field Values

HAPMAP3_KEY

public static final java.lang.String HAPMAP3_KEY

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Constant Field Values

HAPLOTYPE_QUALITY_KEY

public static final java.lang.String HAPLOTYPE_QUALITY_KEY

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Constant Field Values

RMS_MAPPING_QUALITY_KEY

public static final java.lang.String RMS_MAPPING_QUALITY_KEY

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Constant Field Values

MAPPING_QUALITY_ZERO_KEY

public static final java.lang.String MAPPING_QUALITY_ZERO_KEY

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Constant Field Values

SAMPLE_NUMBER_KEY

public static final java.lang.String SAMPLE_NUMBER_KEY

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Constant Field Values

PHASE_QUALITY_KEY

public static final java.lang.String PHASE_QUALITY_KEY

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Constant Field Values

PHASE_SET_KEY

public static final java.lang.String PHASE_SET_KEY

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Constant Field Values

OLD_DEPTH_KEY

public static final java.lang.String OLD_DEPTH_KEY

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Constant Field Values

STRAND_BIAS_KEY

public static final java.lang.String STRAND_BIAS_KEY

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Constant Field Values

SOMATIC_KEY

public static final java.lang.String SOMATIC_KEY

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Constant Field Values

VALIDATED_KEY

public static final java.lang.String VALIDATED_KEY

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Constant Field Values

THOUSAND_GENOMES_KEY

public static final java.lang.String THOUSAND_GENOMES_KEY

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Constant Field Values

SVTYPE

public static final java.lang.String SVTYPE

INFO Type of structural variant

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Constant Field Values

FORMAT_FIELD_SEPARATOR

public static final java.lang.String FORMAT_FIELD_SEPARATOR

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Constant Field Values

GENOTYPE_FIELD_SEPARATOR

public static final java.lang.String GENOTYPE_FIELD_SEPARATOR

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Constant Field Values

GENOTYPE_FIELD_SEPARATOR_CHAR

public static final char GENOTYPE_FIELD_SEPARATOR_CHAR

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Constant Field Values

FIELD_SEPARATOR

public static final java.lang.String FIELD_SEPARATOR

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Constant Field Values

FIELD_SEPARATOR_CHAR

public static final char FIELD_SEPARATOR_CHAR

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Constant Field Values

FILTER_CODE_SEPARATOR

public static final java.lang.String FILTER_CODE_SEPARATOR

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Constant Field Values

INFO_FIELD_ARRAY_SEPARATOR

public static final java.lang.String INFO_FIELD_ARRAY_SEPARATOR

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Constant Field Values

INFO_FIELD_ARRAY_SEPARATOR_CHAR

public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR

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Constant Field Values

ID_FIELD_SEPARATOR

public static final java.lang.String ID_FIELD_SEPARATOR

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Constant Field Values

INFO_FIELD_SEPARATOR

public static final java.lang.String INFO_FIELD_SEPARATOR

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Constant Field Values

INFO_FIELD_SEPARATOR_CHAR

public static final char INFO_FIELD_SEPARATOR_CHAR

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Constant Field Values

UNPHASED

public static final java.lang.String UNPHASED

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Constant Field Values

PHASED

public static final java.lang.String PHASED

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Constant Field Values

PHASED_SWITCH_PROB_v3

public static final java.lang.String PHASED_SWITCH_PROB_v3

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Constant Field Values

PHASING_TOKENS

public static final java.lang.String PHASING_TOKENS

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Constant Field Values

FILTER_HEADER_START

public static final java.lang.String FILTER_HEADER_START

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Constant Field Values

FORMAT_HEADER_START

public static final java.lang.String FORMAT_HEADER_START

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Constant Field Values

INFO_HEADER_START

public static final java.lang.String INFO_HEADER_START

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Constant Field Values

ALT_HEADER_START

public static final java.lang.String ALT_HEADER_START

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Constant Field Values

CONTIG_HEADER_KEY

public static final java.lang.String CONTIG_HEADER_KEY

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Constant Field Values

CONTIG_HEADER_START

public static final java.lang.String CONTIG_HEADER_START

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Constant Field Values

DELETION_ALLELE_v3

public static final char DELETION_ALLELE_v3

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Constant Field Values

INSERTION_ALLELE_v3

public static final char INSERTION_ALLELE_v3

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Constant Field Values

SPANNING_DELETION_ALLELE

public static final char SPANNING_DELETION_ALLELE

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Constant Field Values

NO_CALL_ALLELE

public static final char NO_CALL_ALLELE

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Constant Field Values

NULL_ALLELE

public static final char NULL_ALLELE

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Constant Field Values

UNFILTERED

public static final java.lang.String UNFILTERED

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Constant Field Values

PASSES_FILTERS_v3

public static final java.lang.String PASSES_FILTERS_v3

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Constant Field Values

PASSES_FILTERS_v4

public static final java.lang.String PASSES_FILTERS_v4

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Constant Field Values

EMPTY_ID_FIELD

public static final java.lang.String EMPTY_ID_FIELD

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Constant Field Values

EMPTY_INFO_FIELD

public static final java.lang.String EMPTY_INFO_FIELD

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Constant Field Values

EMPTY_ALTERNATE_ALLELE_FIELD

public static final java.lang.String EMPTY_ALTERNATE_ALLELE_FIELD

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Constant Field Values

MISSING_VALUE_v4

public static final java.lang.String MISSING_VALUE_v4

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Constant Field Values

MISSING_QUALITY_v3

public static final java.lang.String MISSING_QUALITY_v3

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Constant Field Values

MISSING_QUALITY_v3_DOUBLE

public static final java.lang.Double MISSING_QUALITY_v3_DOUBLE

MISSING_GENOTYPE_QUALITY_v3

public static final java.lang.String MISSING_GENOTYPE_QUALITY_v3

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Constant Field Values

MISSING_HAPLOTYPE_QUALITY_v3

public static final java.lang.String MISSING_HAPLOTYPE_QUALITY_v3

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Constant Field Values

MISSING_DEPTH_v3

public static final java.lang.String MISSING_DEPTH_v3

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Constant Field Values

UNBOUNDED_ENCODING_v4

public static final java.lang.String UNBOUNDED_ENCODING_v4

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Constant Field Values

UNBOUNDED_ENCODING_v3

public static final java.lang.String UNBOUNDED_ENCODING_v3

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Constant Field Values

PER_ALTERNATE_COUNT

public static final java.lang.String PER_ALTERNATE_COUNT

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Constant Field Values

PER_ALLELE_COUNT

public static final java.lang.String PER_ALLELE_COUNT

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Constant Field Values

PER_GENOTYPE_COUNT

public static final java.lang.String PER_GENOTYPE_COUNT

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Constant Field Values

EMPTY_ALLELE

public static final java.lang.String EMPTY_ALLELE

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Constant Field Values

EMPTY_GENOTYPE

public static final java.lang.String EMPTY_GENOTYPE

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Constant Field Values

MAX_GENOTYPE_QUAL

public static final int MAX_GENOTYPE_QUAL

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Constant Field Values

VCF_ENCODING_EPSILON

public static final java.lang.Double VCF_ENCODING_EPSILON

Constructor Detail

VCFConstants

public VCFConstants()