picard.vcf

Class GenotypeConcordanceCounts

java.lang.Object

picard.vcf.GenotypeConcordanceCounts

public class GenotypeConcordanceCounts
extends java.lang.Object

A class to store the counts for various truth and call state classifications relative to a reference. With these counts and a provided scheme, summary metrics can be returned.

Constructor Summary

Constructors

Constructor and Description
GenotypeConcordanceCounts()

Method Summary

Methods

Modifier and Type	Method and Description
java.util.Map<picard.vcf.GenotypeConcordanceStates.ContingencyState,java.lang.Integer>	getContingencyStateCounts(GenotypeConcordanceScheme scheme) Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
int	getCount(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Returns the count defined by the truth state set and call state set.
int	getCount(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState) Returns the count defined by the truth state set and call state set.
double	getPpv(GenotypeConcordanceScheme scheme) Returns the PPV defined by the scheme across all call states.
double	getSensitivity(GenotypeConcordanceScheme scheme) Returns the sensitivity defined by the scheme across all truth states.
double	getSensitivity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray) Returns the sensitivity defined by the scheme across the subset of truth states.
double	getSpecificity(GenotypeConcordanceScheme scheme) Returns the specificity defined by the scheme across all truth states.
double	getSpecificity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray) Returns the specificity defined by the scheme across the subset of truth states.
int	getSum() Returns the sum of all pairs of tuples defined by the truth state set and call state set.
int	getSum(java.util.Set<GenotypeConcordanceStates.TruthState> truthStateSet, java.util.Set<picard.vcf.GenotypeConcordanceStates.CallState> callStateSet) Returns the sum of all pairs of tuples defined by the truth state set and call state set.
void	increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Increments a count for the truth/call state tuple.
double	Ppv(GenotypeConcordanceScheme scheme, picard.vcf.GenotypeConcordanceStates.CallState[] callStateList) Returns the PPV defined by the scheme across the subset of call states.
void	validateCountsAgainstScheme(GenotypeConcordanceScheme scheme) Validates that there are no counts for NA states in the underlying scheme

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeConcordanceCounts

public GenotypeConcordanceCounts()

Method Detail

increment

public void increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

Increments a count for the truth/call state tuple.

Parameters:

truthAndCallStates -

validateCountsAgainstScheme

public void validateCountsAgainstScheme(GenotypeConcordanceScheme scheme)

Validates that there are no counts for NA states in the underlying scheme

getSensitivity

public double getSensitivity(GenotypeConcordanceScheme scheme,
                    GenotypeConcordanceStates.TruthState[] truthStateArray)

Returns the sensitivity defined by the scheme across the subset of truth states.

getSensitivity

public double getSensitivity(GenotypeConcordanceScheme scheme)

Returns the sensitivity defined by the scheme across all truth states.

Ppv

public double Ppv(GenotypeConcordanceScheme scheme,
         picard.vcf.GenotypeConcordanceStates.CallState[] callStateList)

Returns the PPV defined by the scheme across the subset of call states.

getPpv

public double getPpv(GenotypeConcordanceScheme scheme)

Returns the PPV defined by the scheme across all call states.

getSpecificity

public double getSpecificity(GenotypeConcordanceScheme scheme,
                    GenotypeConcordanceStates.TruthState[] truthStateArray)

Returns the specificity defined by the scheme across the subset of truth states.

getSpecificity

public double getSpecificity(GenotypeConcordanceScheme scheme)

Returns the specificity defined by the scheme across all truth states.

getCount

public int getCount(GenotypeConcordanceStates.TruthState truthState,
           picard.vcf.GenotypeConcordanceStates.CallState callState)

Returns the count defined by the truth state set and call state set.

getCount

public int getCount(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

Returns the count defined by the truth state set and call state set.

getSum

public int getSum(java.util.Set<GenotypeConcordanceStates.TruthState> truthStateSet,
         java.util.Set<picard.vcf.GenotypeConcordanceStates.CallState> callStateSet)

Returns the sum of all pairs of tuples defined by the truth state set and call state set.

getSum

public int getSum()

Returns the sum of all pairs of tuples defined by the truth state set and call state set.

getContingencyStateCounts

public java.util.Map<picard.vcf.GenotypeConcordanceStates.ContingencyState,java.lang.Integer> getContingencyStateCounts(GenotypeConcordanceScheme scheme)

Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.