Package htsjdk.variant.vcf
Class VCFConstants
- java.lang.Object
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- htsjdk.variant.vcf.VCFConstants
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public final class VCFConstants extends Object
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Field Summary
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Constructor Summary
Constructors Constructor Description VCFConstants()
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Field Detail
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VCF_LOCALE
public static final Locale VCF_LOCALE
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ANCESTRAL_ALLELE_KEY
public static final String ANCESTRAL_ALLELE_KEY
- See Also:
- Constant Field Values
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ALLELE_COUNT_KEY
public static final String ALLELE_COUNT_KEY
- See Also:
- Constant Field Values
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ALLELE_FREQUENCY_KEY
public static final String ALLELE_FREQUENCY_KEY
- See Also:
- Constant Field Values
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ALLELE_NUMBER_KEY
public static final String ALLELE_NUMBER_KEY
- See Also:
- Constant Field Values
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RMS_BASE_QUALITY_KEY
public static final String RMS_BASE_QUALITY_KEY
- See Also:
- Constant Field Values
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CIGAR_KEY
public static final String CIGAR_KEY
- See Also:
- Constant Field Values
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DBSNP_KEY
public static final String DBSNP_KEY
- See Also:
- Constant Field Values
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DEPTH_KEY
public static final String DEPTH_KEY
- See Also:
- Constant Field Values
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END_KEY
public static final String END_KEY
- See Also:
- Constant Field Values
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GENOTYPE_FILTER_KEY
public static final String GENOTYPE_FILTER_KEY
- See Also:
- Constant Field Values
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GENOTYPE_KEY
public static final String GENOTYPE_KEY
- See Also:
- Constant Field Values
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GENOTYPE_POSTERIORS_KEY
public static final String GENOTYPE_POSTERIORS_KEY
- See Also:
- Constant Field Values
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GENOTYPE_QUALITY_KEY
public static final String GENOTYPE_QUALITY_KEY
- See Also:
- Constant Field Values
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GENOTYPE_ALLELE_DEPTHS
public static final String GENOTYPE_ALLELE_DEPTHS
- See Also:
- Constant Field Values
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GENOTYPE_PL_KEY
public static final String GENOTYPE_PL_KEY
- See Also:
- Constant Field Values
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EXPECTED_ALLELE_COUNT_KEY
public static final String EXPECTED_ALLELE_COUNT_KEY
- See Also:
- Constant Field Values
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GENOTYPE_LIKELIHOODS_KEY
@Deprecated public static final String GENOTYPE_LIKELIHOODS_KEY
Deprecated.- See Also:
- Constant Field Values
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HAPMAP2_KEY
public static final String HAPMAP2_KEY
- See Also:
- Constant Field Values
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HAPMAP3_KEY
public static final String HAPMAP3_KEY
- See Also:
- Constant Field Values
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HAPLOTYPE_QUALITY_KEY
public static final String HAPLOTYPE_QUALITY_KEY
- See Also:
- Constant Field Values
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RMS_MAPPING_QUALITY_KEY
public static final String RMS_MAPPING_QUALITY_KEY
- See Also:
- Constant Field Values
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MAPPING_QUALITY_ZERO_KEY
public static final String MAPPING_QUALITY_ZERO_KEY
- See Also:
- Constant Field Values
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SAMPLE_NUMBER_KEY
public static final String SAMPLE_NUMBER_KEY
- See Also:
- Constant Field Values
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PHASE_QUALITY_KEY
public static final String PHASE_QUALITY_KEY
- See Also:
- Constant Field Values
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PHASE_SET_KEY
public static final String PHASE_SET_KEY
- See Also:
- Constant Field Values
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OLD_DEPTH_KEY
public static final String OLD_DEPTH_KEY
- See Also:
- Constant Field Values
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STRAND_BIAS_KEY
public static final String STRAND_BIAS_KEY
- See Also:
- Constant Field Values
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SOMATIC_KEY
public static final String SOMATIC_KEY
- See Also:
- Constant Field Values
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VALIDATED_KEY
public static final String VALIDATED_KEY
- See Also:
- Constant Field Values
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THOUSAND_GENOMES_KEY
public static final String THOUSAND_GENOMES_KEY
- See Also:
- Constant Field Values
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SVTYPE
public static final String SVTYPE
INFO Type of structural variant- See Also:
- Constant Field Values
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FORMAT_FIELD_SEPARATOR
public static final String FORMAT_FIELD_SEPARATOR
- See Also:
- Constant Field Values
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GENOTYPE_FIELD_SEPARATOR
public static final String GENOTYPE_FIELD_SEPARATOR
- See Also:
- Constant Field Values
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GENOTYPE_FIELD_SEPARATOR_CHAR
public static final char GENOTYPE_FIELD_SEPARATOR_CHAR
- See Also:
- Constant Field Values
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FIELD_SEPARATOR
public static final String FIELD_SEPARATOR
- See Also:
- Constant Field Values
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FIELD_SEPARATOR_CHAR
public static final char FIELD_SEPARATOR_CHAR
- See Also:
- Constant Field Values
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FILTER_CODE_SEPARATOR
public static final String FILTER_CODE_SEPARATOR
- See Also:
- Constant Field Values
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INFO_FIELD_ARRAY_SEPARATOR
public static final String INFO_FIELD_ARRAY_SEPARATOR
- See Also:
- Constant Field Values
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INFO_FIELD_ARRAY_SEPARATOR_CHAR
public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR
- See Also:
- Constant Field Values
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ID_FIELD_SEPARATOR
public static final String ID_FIELD_SEPARATOR
- See Also:
- Constant Field Values
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INFO_FIELD_SEPARATOR
public static final String INFO_FIELD_SEPARATOR
- See Also:
- Constant Field Values
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INFO_FIELD_SEPARATOR_CHAR
public static final char INFO_FIELD_SEPARATOR_CHAR
- See Also:
- Constant Field Values
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UNPHASED
public static final String UNPHASED
- See Also:
- Constant Field Values
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PHASED
public static final String PHASED
- See Also:
- Constant Field Values
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PHASED_SWITCH_PROB_v3
public static final String PHASED_SWITCH_PROB_v3
- See Also:
- Constant Field Values
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PHASING_TOKENS
public static final String PHASING_TOKENS
- See Also:
- Constant Field Values
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FILTER_HEADER_START
public static final String FILTER_HEADER_START
- See Also:
- Constant Field Values
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FORMAT_HEADER_START
public static final String FORMAT_HEADER_START
- See Also:
- Constant Field Values
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INFO_HEADER_START
public static final String INFO_HEADER_START
- See Also:
- Constant Field Values
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ALT_HEADER_KEY
public static final String ALT_HEADER_KEY
- See Also:
- Constant Field Values
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ALT_HEADER_START
public static final String ALT_HEADER_START
- See Also:
- Constant Field Values
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CONTIG_HEADER_KEY
public static final String CONTIG_HEADER_KEY
- See Also:
- Constant Field Values
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CONTIG_HEADER_START
public static final String CONTIG_HEADER_START
- See Also:
- Constant Field Values
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ALT_HEADER_OFFSET
public static final int ALT_HEADER_OFFSET
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PEDIGREE_HEADER_KEY
public static final String PEDIGREE_HEADER_KEY
- See Also:
- Constant Field Values
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PEDIGREE_HEADER_START
public static final String PEDIGREE_HEADER_START
- See Also:
- Constant Field Values
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PEDIGREE_HEADER_OFFSET
public static final int PEDIGREE_HEADER_OFFSET
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SAMPLE_HEADER_KEY
public static final String SAMPLE_HEADER_KEY
- See Also:
- Constant Field Values
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SAMPLE_HEADER_START
public static final String SAMPLE_HEADER_START
- See Also:
- Constant Field Values
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SAMPLE_HEADER_OFFSET
public static final int SAMPLE_HEADER_OFFSET
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META_HEADER_KEY
public static final String META_HEADER_KEY
- See Also:
- Constant Field Values
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META_HEADER_START
public static final String META_HEADER_START
- See Also:
- Constant Field Values
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META_HEADER_OFFSET
public static final int META_HEADER_OFFSET
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DELETION_ALLELE_v3
public static final char DELETION_ALLELE_v3
- See Also:
- Constant Field Values
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INSERTION_ALLELE_v3
public static final char INSERTION_ALLELE_v3
- See Also:
- Constant Field Values
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SPANNING_DELETION_ALLELE
public static final char SPANNING_DELETION_ALLELE
- See Also:
- Constant Field Values
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NO_CALL_ALLELE
public static final char NO_CALL_ALLELE
- See Also:
- Constant Field Values
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NULL_ALLELE
public static final char NULL_ALLELE
- See Also:
- Constant Field Values
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UNFILTERED
public static final String UNFILTERED
- See Also:
- Constant Field Values
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PASSES_FILTERS_v3
public static final String PASSES_FILTERS_v3
- See Also:
- Constant Field Values
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PASSES_FILTERS_v4
public static final String PASSES_FILTERS_v4
- See Also:
- Constant Field Values
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EMPTY_ID_FIELD
public static final String EMPTY_ID_FIELD
- See Also:
- Constant Field Values
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EMPTY_INFO_FIELD
public static final String EMPTY_INFO_FIELD
- See Also:
- Constant Field Values
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EMPTY_ALTERNATE_ALLELE_FIELD
public static final String EMPTY_ALTERNATE_ALLELE_FIELD
- See Also:
- Constant Field Values
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MISSING_VALUE_v4
public static final String MISSING_VALUE_v4
- See Also:
- Constant Field Values
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MISSING_QUALITY_v3
public static final String MISSING_QUALITY_v3
- See Also:
- Constant Field Values
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MISSING_QUALITY_v3_DOUBLE
public static final Double MISSING_QUALITY_v3_DOUBLE
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MISSING_GENOTYPE_QUALITY_v3
public static final String MISSING_GENOTYPE_QUALITY_v3
- See Also:
- Constant Field Values
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MISSING_HAPLOTYPE_QUALITY_v3
public static final String MISSING_HAPLOTYPE_QUALITY_v3
- See Also:
- Constant Field Values
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MISSING_DEPTH_v3
public static final String MISSING_DEPTH_v3
- See Also:
- Constant Field Values
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UNBOUNDED_ENCODING_v4
public static final String UNBOUNDED_ENCODING_v4
- See Also:
- Constant Field Values
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UNBOUNDED_ENCODING_v3
public static final String UNBOUNDED_ENCODING_v3
- See Also:
- Constant Field Values
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PER_ALTERNATE_COUNT
public static final String PER_ALTERNATE_COUNT
- See Also:
- Constant Field Values
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PER_ALLELE_COUNT
public static final String PER_ALLELE_COUNT
- See Also:
- Constant Field Values
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PER_GENOTYPE_COUNT
public static final String PER_GENOTYPE_COUNT
- See Also:
- Constant Field Values
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EMPTY_ALLELE
public static final String EMPTY_ALLELE
- See Also:
- Constant Field Values
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EMPTY_GENOTYPE
public static final String EMPTY_GENOTYPE
- See Also:
- Constant Field Values
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MAX_GENOTYPE_QUAL
public static final int MAX_GENOTYPE_QUAL
- See Also:
- Constant Field Values
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VCF_ENCODING_EPSILON
public static final Double VCF_ENCODING_EPSILON
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