Package org.pharmgkb.parser.vcf.model.genotype

Class VcfGenotype

java.lang.Object

org.pharmgkb.parser.vcf.model.genotype.VcfGenotype

@Immutable
public class VcfGenotype
extends Object

A diploid (or haploid; see below) genotype matching the VCF 4.2 specification.

For example:

• A/A (an unphased homozygous genotype)
• A|ATG (an phased heterozygous 2bp insertion of TG)

This class can also handle haploid genotypes (e.g. A), but note that:

     Genotype.fromString("A").toString(); // prints A|A
 
 

Always use equals(Object) to compare genotypes, not toString().equals.

Constructor Summary

Constructors

Constructor	Description
VcfGenotype(VcfAllele allele1, VcfAllele allele2, boolean isPhased)	Note:

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
static VcfGenotype	fromNumberString(VcfPosition position, String genotype)
static VcfGenotype	fromString(String genotype)
static VcfGenotype	fromVcf(VcfPosition position, VcfSample sample)
VcfAllele	getAllele1()
VcfAllele	getAllele2()
Set<VcfAllele>	getAlleleSet()
int	hashCode()
boolean	isHomozygous()
boolean	isNoCall()
boolean	isPhased()
String	makeGt(VcfPosition position)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

VcfGenotype

public VcfGenotype(@Nullable
 VcfAllele allele1,
 @Nullable
 VcfAllele allele2,
 boolean isPhased)

Note:

   VcfGenotype homozygous = new VcfGenotype("A", "A", false);
   homogyzgous.isPhased(); // false
 
 

The same logic applies with haploid genotypes.

Method Details

fromString

@Nonnull
public static VcfGenotype fromString(@Nonnull
 String genotype)

Parameters:

genotype - A string like A/TT

fromVcf

@Nullable
public static VcfGenotype fromVcf(@Nonnull
 VcfPosition position,
 @Nonnull
 VcfSample sample)

Returns:

The genotype, or null if GT is null

fromNumberString

public static VcfGenotype fromNumberString(@Nonnull
 VcfPosition position,
 @Nonnull
 String genotype)

Parameters:

genotype - A string like 0/1

Returns:

The genotype, or null if GT is null

makeGt

@Nonnull
public String makeGt(@Nonnull
 VcfPosition position)

isPhased

public boolean isPhased()

Returns:

True if the genotype is effectively phased.: returns true for haploid genotypes and homozygous genotypes

isHomozygous

public boolean isHomozygous()

isNoCall

public boolean isNoCall()

getAllele1

@Nullable
public VcfAllele getAllele1()

getAllele2

@Nullable
public VcfAllele getAllele2()

getAlleleSet

@Nonnull
public Set<VcfAllele> getAlleleSet()

toString

public String toString()

Overrides:

toString in class Object

Returns:

For example, A|ATGC or A/C

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object