public class GenotypeConcordanceCounts extends Object
Constructor and Description |
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GenotypeConcordanceCounts() |
Modifier and Type | Method and Description |
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double |
calculateGenotypeConcordance(GenotypeConcordanceScheme scheme,
boolean missingSitesFlag)
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made
If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
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double |
calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme scheme,
boolean missingSitesFlag)
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made
If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
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Map<picard.vcf.GenotypeConcordanceStates.ContingencyState,Long> |
getContingencyStateCounts(GenotypeConcordanceScheme scheme)
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
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long |
getCount(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
Returns the count defined by the truth state set and call state set.
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long |
getCount(GenotypeConcordanceStates.TruthState truthState,
picard.vcf.GenotypeConcordanceStates.CallState callState)
Returns the count defined by the truth state set and call state set.
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double |
getCounterSize() |
double |
getSensitivity(GenotypeConcordanceScheme scheme,
GenotypeConcordanceStates.TruthState[] truthStateArray)
Returns the sensitivity defined by the scheme across the subset of truth states.
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double |
getSpecificity(GenotypeConcordanceScheme scheme,
GenotypeConcordanceStates.TruthState[] truthStateArray)
Returns the specificity defined by the scheme across the subset of truth states.
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long |
getSum()
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
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long |
getSum(Set<GenotypeConcordanceStates.TruthState> truthStateSet,
Set<picard.vcf.GenotypeConcordanceStates.CallState> callStateSet)
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
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void |
increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
Increments a count for the truth/call state tuple.
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void |
increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates,
double count) |
boolean |
isMissing(GenotypeConcordanceStates.TruthState truthState,
picard.vcf.GenotypeConcordanceStates.CallState callState)
Returns true if EITHER the truth or call state is MISSING.
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boolean |
isVar(GenotypeConcordanceStates.TruthState truthState,
picard.vcf.GenotypeConcordanceStates.CallState callState)
Returns true if EITHER the truth or call state is a VAR.
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double |
Ppv(GenotypeConcordanceScheme scheme,
picard.vcf.GenotypeConcordanceStates.CallState[] callStateList)
Returns the PPV defined by the scheme across the subset of call states.
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void |
validateCountsAgainstScheme(GenotypeConcordanceScheme scheme)
Validates that there are no counts for NA states in the underlying scheme
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public void increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
truthAndCallStates
- public void increment(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates, double count)
public double getCounterSize()
public void validateCountsAgainstScheme(GenotypeConcordanceScheme scheme)
public double calculateGenotypeConcordance(GenotypeConcordanceScheme scheme, boolean missingSitesFlag)
public double calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme scheme, boolean missingSitesFlag)
public double getSensitivity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray)
public double Ppv(GenotypeConcordanceScheme scheme, picard.vcf.GenotypeConcordanceStates.CallState[] callStateList)
public double getSpecificity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray)
public long getCount(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState)
public long getCount(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
public boolean isVar(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState)
public boolean isMissing(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState)
public long getSum(Set<GenotypeConcordanceStates.TruthState> truthStateSet, Set<picard.vcf.GenotypeConcordanceStates.CallState> callStateSet)
public long getSum()
public Map<picard.vcf.GenotypeConcordanceStates.ContingencyState,Long> getContingencyStateCounts(GenotypeConcordanceScheme scheme)