picard.vcf

Enum GenotypeConcordanceStates.CallState

java.lang.Object

java.lang.Enum<GenotypeConcordanceStates.CallState>

picard.vcf.GenotypeConcordanceStates.CallState

All Implemented Interfaces:

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

Enclosing class:

GenotypeConcordanceStates

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

These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence. The Enum constants must be in the same order as the truth state to allow for comparison.

Enum Constant Summary

Enum Constants

Enum Constant and Description
GT_FILTERED
HET_REF_VAR1
HET_REF_VAR2
HET_REF_VAR3
HET_VAR1_VAR2
HET_VAR1_VAR3
HET_VAR3_VAR4
HOM_REF
HOM_VAR1
HOM_VAR2
HOM_VAR3
IS_MIXED
LOW_DP
LOW_GQ
MISSING
NO_CALL
VC_FILTERED

Method Summary

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

HOM_REF

public static final GenotypeConcordanceStates.CallState HOM_REF

HET_REF_VAR1

public static final GenotypeConcordanceStates.CallState HET_REF_VAR1

HET_VAR1_VAR2

public static final GenotypeConcordanceStates.CallState HET_VAR1_VAR2

HOM_VAR1

public static final GenotypeConcordanceStates.CallState HOM_VAR1

HET_REF_VAR2

public static final GenotypeConcordanceStates.CallState HET_REF_VAR2

HET_REF_VAR3

public static final GenotypeConcordanceStates.CallState HET_REF_VAR3

HET_VAR1_VAR3

public static final GenotypeConcordanceStates.CallState HET_VAR1_VAR3

HET_VAR3_VAR4

public static final GenotypeConcordanceStates.CallState HET_VAR3_VAR4

HOM_VAR2

public static final GenotypeConcordanceStates.CallState HOM_VAR2

HOM_VAR3

public static final GenotypeConcordanceStates.CallState HOM_VAR3

NO_CALL

public static final GenotypeConcordanceStates.CallState NO_CALL

LOW_GQ

public static final GenotypeConcordanceStates.CallState LOW_GQ

LOW_DP

public static final GenotypeConcordanceStates.CallState LOW_DP

VC_FILTERED

public static final GenotypeConcordanceStates.CallState VC_FILTERED

GT_FILTERED

public static final GenotypeConcordanceStates.CallState GT_FILTERED

IS_MIXED

public static final GenotypeConcordanceStates.CallState IS_MIXED

Method Detail

values

public static GenotypeConcordanceStates.CallState[] 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.CallState c : GenotypeConcordanceStates.CallState.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.CallState 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.CallState getHom(int alleleIdx)

getHet

public static GenotypeConcordanceStates.CallState getHet(int allele0idx,
                                                         int allele1idx)

getCode

public int getCode()