picard.vcf

Enum GenotypeConcordanceStates.TruthState

java.lang.Object

java.lang.Enum<GenotypeConcordanceStates.TruthState>

picard.vcf.GenotypeConcordanceStates.TruthState

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<GenotypeConcordanceStates.TruthState>

Enclosing class:

GenotypeConcordanceStates

public static enum GenotypeConcordanceStates.TruthState
extends java.lang.Enum<GenotypeConcordanceStates.TruthState>

These states represent the relationship between a truth genotype and the reference sequence.

Enum Constant Summary

Enum Constants

Enum Constant and Description
GT_FILTERED
HET_REF_VAR1
HET_VAR1_VAR2
HOM_REF
HOM_VAR1
IS_MIXED
LOW_DP
LOW_GQ
MISSING
NO_CALL
VC_FILTERED

Method Summary

Modifier and Type	Method and Description
int	getCode()
static GenotypeConcordanceStates.TruthState	getHom(int alleleIdx)
static GenotypeConcordanceStates.TruthState	getVar(int allele0idx, int allele1idx)
static GenotypeConcordanceStates.TruthState	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static GenotypeConcordanceStates.TruthState[]	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

MISSING

public static final GenotypeConcordanceStates.TruthState MISSING

HOM_REF

public static final GenotypeConcordanceStates.TruthState HOM_REF

HET_REF_VAR1

public static final GenotypeConcordanceStates.TruthState HET_REF_VAR1

HET_VAR1_VAR2

public static final GenotypeConcordanceStates.TruthState HET_VAR1_VAR2

HOM_VAR1

public static final GenotypeConcordanceStates.TruthState HOM_VAR1

NO_CALL

public static final GenotypeConcordanceStates.TruthState NO_CALL

LOW_GQ

public static final GenotypeConcordanceStates.TruthState LOW_GQ

LOW_DP

public static final GenotypeConcordanceStates.TruthState LOW_DP

VC_FILTERED

public static final GenotypeConcordanceStates.TruthState VC_FILTERED

GT_FILTERED

public static final GenotypeConcordanceStates.TruthState GT_FILTERED

IS_MIXED

public static final GenotypeConcordanceStates.TruthState IS_MIXED

Method Detail

values

public static GenotypeConcordanceStates.TruthState[] 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 (GenotypeConcordanceStates.TruthState c : GenotypeConcordanceStates.TruthState.values())
    System.out.println(c);

Returns:

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

valueOf

public static GenotypeConcordanceStates.TruthState 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

getHom

public static GenotypeConcordanceStates.TruthState getHom(int alleleIdx)

getVar

public static GenotypeConcordanceStates.TruthState getVar(int allele0idx,
                                                          int allele1idx)

getCode

public int getCode()