Package picard.vcf
Class GenotypeConcordanceScheme
- java.lang.Object
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- picard.vcf.GenotypeConcordanceScheme
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- Direct Known Subclasses:
GA4GHScheme
,GA4GHSchemeWithMissingAsHomRef
public abstract class GenotypeConcordanceScheme extends Object
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
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Constructor Summary
Constructors Constructor Description GenotypeConcordanceScheme()
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Method Summary
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Field Detail
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scheme
protected final Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]> scheme
The underlying scheme
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NA
public static final GenotypeConcordanceStates.ContingencyState[] NA
These are convenience variables for defining a scheme. NA means that such a tuple should never be observed.
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EMPTY
protected static final GenotypeConcordanceStates.ContingencyState[] EMPTY
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TP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TP_ONLY
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FP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FP_ONLY
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TN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TN_ONLY
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FN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FN_ONLY
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TP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FN
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TP_FP
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP
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TP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_TN
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FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_FN
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FP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN
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FP_TN_FN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN_FN
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TP_FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP_FN
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TN_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TN_FN
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Method Detail
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initiateScheme
protected abstract void initiateScheme()
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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.
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getConcordanceStateArray
public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
Get the concordance state array associate with the given truth state and call state tuple.
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getContingencyStateString
public String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)
Get the contingency state array as a parse-able string
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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
public void validateScheme() throws PicardException
Check that all cells in the scheme exist.- Throws:
PicardException
- if a missing tuple was found.
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