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