Package htsjdk.variant.variantcontext

Class FastGenotype

java.lang.Object

htsjdk.variant.variantcontext.Genotype

htsjdk.variant.variantcontext.FastGenotype

All Implemented Interfaces:

Serializable, Comparable<Genotype>

public final class FastGenotype
extends Genotype

This class encompasses all the basic information about a genotype. For the sake of performance, it does not make a copy of the Collections/arrays it's constructed from, and so subsequent changes to those Collections/arrays will be reflected in the FastGenotype object A genotype has several key fields

• a sample name, must be a non-null string
• an ordered list of alleles, intrepreted as the genotype of the sample, each allele for each chromosome given in order. If alleles = [a*, t] then the sample is a/t, with a (the reference from the *) the first chromosome and t on the second chromosome
• an isPhased marker indicating where the alleles are phased with respect to some global coordinate system. See VCF4.1 spec for a detailed discussion
• Inline, optimized ints and int[] values for:
  • GQ: the phred-scaled genotype quality, or -1 if it's missing
  • DP: the count of reads at this locus for this sample, or -1 if missing
  • AD: an array of counts of reads at this locus, one for each Allele at the site, that is, for each allele in the surrounding VariantContext. null if missing.
  • PL: phred-scaled genotype likelihoods in standard VCF4.1 order for all combinations of the alleles in the surrounding VariantContext, given the ploidy of the sample (from the alleles vector). null if missing.
• A general map from String keys to -> Object values for all other attributes in this genotype. Note that this map should not contain duplicate values for the standard bindings for GQ, DP, AD, and PL. Genotype filters can be put into this genotype, but it isn't respected by the GATK in analyses

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.

Since:

05/12

See Also:

• Serialized Form

Field Summary

Fields inherited from class htsjdk.variant.variantcontext.Genotype

PHASED_ALLELE_SEPARATOR, PRIMARY_KEYS, serialVersionUID, UNPHASED_ALLELE_SEPARATOR

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	FastGenotype(String sampleName, List<Allele> alleles, boolean isPhased, int GQ, int DP, int[] AD, int[] PL, String filters, Map<String,Object> extendedAttributes)	The only way to make one of these, for use by GenotypeBuilder only

Method Summary

Modifier and Type	Method	Description
int[]	getAD()
Allele	getAllele(int i)	Get the ith allele in this genotype
List<Allele>	getAlleles()
int	getDP()
Map<String,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.

Methods inherited from class htsjdk.variant.variantcontext.Genotype

compareTo, countAllele, determineType, getAlleleStrings, getAnyAttribute, getAttributeAsDouble, getAttributeAsInt, getAttributeAsString, getExtendedAttribute, getExtendedAttribute, getFilters, getGenotypeString, getGenotypeString, getLikelihoods, getLikelihoodsString, getLog10PError, getPhredScaledQual, getPloidy, getSampleName, getType, hasAD, hasAltAllele, hasAnyAttribute, hasDP, hasExtendedAttribute, hasForbiddenKey, hasGQ, hasLikelihoods, hasLog10PError, hasPL, hasRefAllele, isAvailable, isCalled, isFiltered, isForbiddenKey, isHet, isHetNonRef, isHom, isHomRef, isHomVar, isMixed, isNoCall, isNonInformative, sameGenotype, sameGenotype, sortedString, toBriefString, toString, toStringIfExists, toStringIfExists, toStringIfExists

Methods inherited from class java.lang.Object

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

Constructor Details

FastGenotype

protected FastGenotype(String sampleName,
 List<Allele> alleles,
 boolean isPhased,
 int GQ,
 int DP,
 int[] AD,
 int[] PL,
 String filters,
 Map<String,Object> extendedAttributes)

The only way to make one of these, for use by GenotypeBuilder only

Parameters:

sampleName -

alleles -

isPhased -

GQ -

DP -

AD -

PL -

extendedAttributes -

Method Details

getAlleles

public List<Allele> getAlleles()

Specified by:

getAlleles in class Genotype

Returns:

the alleles for this genotype. Cannot be null. May be empty

getAllele

public Allele getAllele(int i)

Description copied from class: Genotype

Get the ith allele in this genotype

Specified by:

getAllele in class Genotype

Parameters:

i - the ith allele, must be < the ploidy, starting with 0

Returns:

the allele at position i, which cannot be null

isPhased

public boolean isPhased()

Description copied from class: Genotype

Are the alleles phased w.r.t. the global phasing system?

Specified by:

isPhased in class Genotype

Returns:

true if yes

getDP

public int getDP()

Specified by:

getDP in class Genotype

Returns:

the sequencing depth of this sample, or -1 if this value is missing

getAD

public int[] getAD()

Specified by:

getAD in class Genotype

Returns:

the count of reads, one for each allele in the surrounding Variant context, matching the corresponding allele, or null if this value is missing. MUST NOT BE MODIFIED!

getGQ

public int getGQ()

Description copied from class: Genotype

Returns a phred-scaled quality score, or -1 if none is available

Specified by:

getGQ in class Genotype

Returns:

getPL

public int[] getPL()

Description copied from class: Genotype

Unsafe low-level accessor the PL field itself, may be null.

Specified by:

getPL in class Genotype

Returns:

a pointer to the underlying PL data. MUST NOT BE MODIFIED!

getExtendedAttributes

public Map<String,Object> getExtendedAttributes()

Description copied from class: Genotype

Returns the extended attributes for this object

Specified by:

getExtendedAttributes in class Genotype

Returns:

is never null, but is often isEmpty()