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