picard.vcf

Class GenotypeConcordanceScheme

java.lang.Object

picard.vcf.GenotypeConcordanceScheme

Direct Known Subclasses:

GA4GHScheme, GA4GHSchemeWithMissingAsHomRef

public abstract class GenotypeConcordanceScheme
extends java.lang.Object

This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.

Field Summary

Fields

Modifier and Type	Field and Description
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	EMPTY
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	FN_ONLY
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	FP_FN
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	FP_ONLY
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	FP_TN
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	FP_TN_FN
static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	NA These are convenience variables for defining a scheme.
protected java.util.Map<picard.vcf.GenotypeConcordanceStates.TruthAndCallStates,picard.vcf.GenotypeConcordanceStates.ContingencyState[]>	scheme The underlying scheme
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TN_FN
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TN_ONLY
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TP_FN
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TP_FP
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TP_FP_FN
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TP_ONLY
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[]	TP_TN

Constructor Summary

Constructors

Constructor and Description
GenotypeConcordanceScheme()

Method Summary

Modifier and Type	Method and Description
protected void	addRow(picard.vcf.GenotypeConcordanceStates.CallState callState, picard.vcf.GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays) Adds a row to the scheme
picard.vcf.GenotypeConcordanceStates.ContingencyState[]	getConcordanceStateArray(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Get the concordance state array associate with the given truth state and call state tuple.
picard.vcf.GenotypeConcordanceStates.ContingencyState[]	getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState) Get the concordance state array associate with the given truth state and call state tuple.
java.util.Set<picard.vcf.GenotypeConcordanceStates.ContingencyState>	getContingencyStateSet(picard.vcf.GenotypeConcordanceStates.ContingencyState[] contingencyStateArray) Get the contingency state array as a set
java.lang.String	getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState) Get the contingency state array as a parse-able string
protected abstract void	initiateScheme()
void	validateScheme() Check that all cells in the scheme exist.

Methods inherited from class java.lang.Object

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

Field Detail

scheme

protected final java.util.Map<picard.vcf.GenotypeConcordanceStates.TruthAndCallStates,picard.vcf.GenotypeConcordanceStates.ContingencyState[]> scheme

The underlying scheme

NA

public static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] NA

These are convenience variables for defining a scheme. NA means that such a tuple should never be observed.

EMPTY

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] EMPTY

TP_ONLY

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_ONLY

FP_ONLY

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_ONLY

TN_ONLY

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TN_ONLY

FN_ONLY

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FN_ONLY

TP_FN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FN

TP_FP

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FP

TP_TN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_TN

FP_FN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_FN

FP_TN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_TN

FP_TN_FN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_TN_FN

TP_FP_FN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FP_FN

TN_FN

protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TN_FN

Constructor Detail

GenotypeConcordanceScheme

public GenotypeConcordanceScheme()

Method Detail

initiateScheme

protected abstract void initiateScheme()

addRow

protected void addRow(picard.vcf.GenotypeConcordanceStates.CallState callState,
                      picard.vcf.GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)

Adds a row to the scheme

Parameters:

callState - the call state (row)

concordanceStateArrays - the concordance state arrays for each truth value, in order

getConcordanceStateArray

public picard.vcf.GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState,
                                                                                        picard.vcf.GenotypeConcordanceStates.CallState callState)

Get the concordance state array associate with the given truth state and call state tuple.

getConcordanceStateArray

public picard.vcf.GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

Get the concordance state array associate with the given truth state and call state tuple.

getContingencyStateString

public java.lang.String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState,
                                                  picard.vcf.GenotypeConcordanceStates.CallState callState)

Get the contingency state array as a parse-able string

getContingencyStateSet

public java.util.Set<picard.vcf.GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(picard.vcf.GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)

Get the contingency state array as a set

Parameters:

contingencyStateArray -

Returns:

validateScheme

public void validateScheme()
                    throws PicardException

Check that all cells in the scheme exist.

Throws:

PicardException - if a missing tuple was found.