htsjdk.variant.variantcontext

Enum GenotypeType

java.lang.Object

java.lang.Enum<GenotypeType>

htsjdk.variant.variantcontext.GenotypeType

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<GenotypeType>

public enum GenotypeType
extends java.lang.Enum<GenotypeType>

Summary types for Genotype objects

Since:

Date created

Enum Constant Summary

Enum Constants

Enum Constant and Description
HET The sample is heterozygous, with at least one ref and at least one one alt in any order
HOM_REF The sample is homozygous reference
HOM_VAR All alleles are non-reference
MIXED Some chromosomes are NO_CALL and others are called
NO_CALL The sample is no-called (all alleles are NO_CALL
UNAVAILABLE There is no allele data availble for this sample (alleles.isEmpty)

Method Summary

Methods

Modifier and Type	Method and Description
static GenotypeType	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static GenotypeType[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

NO_CALL

public static final GenotypeType NO_CALL

The sample is no-called (all alleles are NO_CALL

HOM_REF

public static final GenotypeType HOM_REF

The sample is homozygous reference

HET

public static final GenotypeType HET

The sample is heterozygous, with at least one ref and at least one one alt in any order

HOM_VAR

public static final GenotypeType HOM_VAR

All alleles are non-reference

UNAVAILABLE

public static final GenotypeType UNAVAILABLE

There is no allele data availble for this sample (alleles.isEmpty)

MIXED

public static final GenotypeType MIXED

Some chromosomes are NO_CALL and others are called

Method Detail

values

public static GenotypeType[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (GenotypeType c : GenotypeType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static GenotypeType valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null