GA4GHScheme
, GA4GHSchemeWithMissingAsHomRef
public abstract class GenotypeConcordanceScheme extends Object
Constructor | Description |
---|---|
GenotypeConcordanceScheme() |
protected final Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]> scheme
public static final GenotypeConcordanceStates.ContingencyState[] NA
protected static final GenotypeConcordanceStates.ContingencyState[] EMPTY
protected static final GenotypeConcordanceStates.ContingencyState[] TP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP
protected static final GenotypeConcordanceStates.ContingencyState[] TP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TN_FN
protected abstract void initiateScheme()
protected void addRow(GenotypeConcordanceStates.CallState callState, GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
callState
- the call state (row)concordanceStateArrays
- the concordance state arrays for each truth value, in orderpublic GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)
public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
public String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)
public Set<GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)
contingencyStateArray
- public void validateScheme() throws PicardException
PicardException
- if a missing tuple was found.