Package | Description |
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picard.vcf |
Modifier and Type | Field and Description |
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GenotypeConcordanceStates.CallState |
GenotypeConcordanceDetailMetrics.CALL_STATE
The state of the 'call' sample (i.e.
|
GenotypeConcordanceStates.CallState |
GenotypeConcordanceStates.TruthAndCallStates.callState |
Modifier and Type | Method and Description |
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static GenotypeConcordanceStates.CallState |
GenotypeConcordanceStates.CallState.getHet(int allele0idx,
int allele1idx) |
static GenotypeConcordanceStates.CallState |
GenotypeConcordanceStates.CallState.getHom(int alleleIdx) |
static GenotypeConcordanceStates.CallState |
GenotypeConcordanceStates.CallState.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static GenotypeConcordanceStates.CallState[] |
GenotypeConcordanceStates.CallState.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
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protected void |
GenotypeConcordanceScheme.addRow(GenotypeConcordanceStates.CallState callState,
GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
Adds a row to the scheme
|
GenotypeConcordanceStates.ContingencyState[] |
GenotypeConcordanceScheme.getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Get the concordance state array associate with the given truth state and call state tuple.
|
java.lang.String |
GenotypeConcordanceScheme.getContingencyStateString(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Get the contingency state array as a parse-able string
|
long |
GenotypeConcordanceCounts.getCount(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Returns the count defined by the truth state set and call state set.
|
boolean |
GenotypeConcordanceCounts.isMissing(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Returns true if EITHER the truth or call state is MISSING.
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boolean |
GenotypeConcordanceCounts.isVar(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Returns true if EITHER the truth or call state is a VAR.
|
double |
GenotypeConcordanceCounts.Ppv(GenotypeConcordanceScheme scheme,
GenotypeConcordanceStates.CallState[] callStateList)
Returns the PPV defined by the scheme across the subset of call states.
|
Modifier and Type | Method and Description |
---|---|
long |
GenotypeConcordanceCounts.getSum(java.util.Set<GenotypeConcordanceStates.TruthState> truthStateSet,
java.util.Set<GenotypeConcordanceStates.CallState> callStateSet)
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
|
Constructor and Description |
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TruthAndCallStates(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState) |