public final class FastGenotype extends Genotype
isPhased marker indicating where the alleles are phased with respect to some global
coordinate system. See VCF4.1 spec for a detailed discussionints and int[] values for:
-1 if it's missing-1 if missingVariantContext. null if missing.VariantContext, given
the ploidy of the sample (from the alleles vector). null if missing.The only way to build a Genotype object is with a GenotypeBuilder, which permits values
to be set in any order, which means that GenotypeBuilder may at some in the chain of
sets pass through invalid states that are not permitted in a fully formed immutable
Genotype.
Note this is a simplified, refactored Genotype object based on the original generic (and slow) implementation from the original VariantContext + Genotype codebase.
PHASED_ALLELE_SEPARATOR, PRIMARY_KEYS, serialVersionUID, UNPHASED_ALLELE_SEPARATOR| Modifier | Constructor and Description |
|---|---|
protected |
FastGenotype(java.lang.String sampleName,
java.util.List<Allele> alleles,
boolean isPhased,
int GQ,
int DP,
int[] AD,
int[] PL,
java.lang.String filters,
java.util.Map<java.lang.String,java.lang.Object> extendedAttributes)
The only way to make one of these, for use by GenotypeBuilder only
|
| Modifier and Type | Method and Description |
|---|---|
int[] |
getAD() |
Allele |
getAllele(int i)
Get the ith allele in this genotype
|
java.util.List<Allele> |
getAlleles() |
int |
getDP() |
java.util.Map<java.lang.String,java.lang.Object> |
getExtendedAttributes()
Returns the extended attributes for this object
|
int |
getGQ()
Returns a phred-scaled quality score, or -1 if none is available
|
int[] |
getPL()
Unsafe low-level accessor the PL field itself, may be null.
|
boolean |
isPhased()
Are the alleles phased w.r.t.
|
compareTo, countAllele, determineType, getAlleleStrings, getAnyAttribute, getAttributeAsDouble, getAttributeAsInt, getAttributeAsString, getExtendedAttribute, getExtendedAttribute, getFilters, getGenotypeString, getGenotypeString, getLikelihoods, getLikelihoodsString, getLog10PError, getPhredScaledQual, getPloidy, getSampleName, getType, hasAD, hasAnyAttribute, hasDP, hasExtendedAttribute, hasForbiddenKey, hasGQ, hasLikelihoods, hasLog10PError, hasPL, isAvailable, isCalled, isFiltered, isForbiddenKey, isHet, isHetNonRef, isHom, isHomRef, isHomVar, isMixed, isNoCall, isNonInformative, sameGenotype, sameGenotype, sortedString, toBriefString, toString, toStringIfExists, toStringIfExists, toStringIfExistsprotected FastGenotype(java.lang.String sampleName,
java.util.List<Allele> alleles,
boolean isPhased,
int GQ,
int DP,
int[] AD,
int[] PL,
java.lang.String filters,
java.util.Map<java.lang.String,java.lang.Object> extendedAttributes)
sampleName - alleles - isPhased - GQ - DP - AD - PL - extendedAttributes - public java.util.List<Allele> getAlleles()
getAlleles in class Genotypepublic Allele getAllele(int i)
Genotypepublic boolean isPhased()
Genotypepublic int getDP()
public int[] getAD()
public int getGQ()
Genotypepublic int[] getPL()
Genotypepublic java.util.Map<java.lang.String,java.lang.Object> getExtendedAttributes()
GenotypegetExtendedAttributes in class Genotype