Package picard.vcf
Class GenotypeConcordanceScheme
java.lang.Object
picard.vcf.GenotypeConcordanceScheme
- Direct Known Subclasses:
GA4GHScheme,GA4GHSchemeWithMissingAsHomRef
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]static final GenotypeConcordanceStates.ContingencyState[]These are convenience variables for defining a scheme.protected final Map<GenotypeConcordanceStates.TruthAndCallStates, GenotypeConcordanceStates.ContingencyState[]> The underlying schemeprotected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[]protected static final GenotypeConcordanceStates.ContingencyState[] -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidaddRow(GenotypeConcordanceStates.CallState callState, GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays) Adds a row to the schemegetConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Get the concordance state array associate with the given truth state and call state tuple.getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the concordance state array associate with the given truth state and call state tuple.getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray) Get the contingency state array as a setgetContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the contingency state array as a parse-able stringprotected abstract voidvoidCheck that all cells in the scheme exist.
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Field Details
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scheme
protected final Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]> schemeThe underlying scheme -
NA
These are convenience variables for defining a scheme. NA means that such a tuple should never be observed. -
EMPTY
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TP_ONLY
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FP_ONLY
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TN_ONLY
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FN_ONLY
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TP_FN
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TP_FP
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TP_TN
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FP_FN
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FP_TN
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FP_TN_FN
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TP_FP_FN
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TN_FN
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Constructor Details
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GenotypeConcordanceScheme
public GenotypeConcordanceScheme()
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Method Details
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initiateScheme
protected abstract void initiateScheme() -
addRow
protected void addRow(GenotypeConcordanceStates.CallState callState, 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
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getConcordanceStateArray
public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the concordance state array associate with the given truth state and call state tuple. -
getConcordanceStateArray
public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Get the concordance state array associate with the given truth state and call state tuple. -
getContingencyStateString
public String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the contingency state array as a parse-able string -
getContingencyStateSet
public Set<GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray) Get the contingency state array as a set- Parameters:
contingencyStateArray-- Returns:
- contingency state array (as a Set)
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validateScheme
Check that all cells in the scheme exist.- Throws:
PicardException- if a missing tuple was found.
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