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[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addRow
(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 void
void
Check 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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