public abstract class GenotypeConcordanceScheme extends Object
Modifier and Type | Field and Description |
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protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
EMPTY |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
FN_ONLY |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
FP_FN |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
FP_ONLY |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
FP_TN |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
FP_TN_FN |
static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
NA
These are convenience variables for defining a scheme.
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protected Map<picard.vcf.GenotypeConcordanceStates.TruthAndCallStates,picard.vcf.GenotypeConcordanceStates.ContingencyState[]> |
scheme
The underlying scheme
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protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TN_FN |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TN_ONLY |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TP_FN |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TP_FP |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TP_FP_FN |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TP_ONLY |
protected static picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
TP_TN |
Constructor and Description |
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GenotypeConcordanceScheme() |
Modifier and Type | Method and Description |
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protected void |
addRow(picard.vcf.GenotypeConcordanceStates.CallState callState,
picard.vcf.GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
Adds a row to the scheme
|
picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
getConcordanceStateArray(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
Get the concordance state array associate with the given truth state and call state tuple.
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picard.vcf.GenotypeConcordanceStates.ContingencyState[] |
getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState,
picard.vcf.GenotypeConcordanceStates.CallState callState)
Get the concordance state array associate with the given truth state and call state tuple.
|
Set<picard.vcf.GenotypeConcordanceStates.ContingencyState> |
getContingencyStateSet(picard.vcf.GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)
Get the contingency state array as a set
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String |
getContingencyStateString(GenotypeConcordanceStates.TruthState truthState,
picard.vcf.GenotypeConcordanceStates.CallState callState)
Get the contingency state array as a parse-able string
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protected abstract void |
initiateScheme() |
void |
validateScheme()
Check that all cells in the scheme exist.
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protected final Map<picard.vcf.GenotypeConcordanceStates.TruthAndCallStates,picard.vcf.GenotypeConcordanceStates.ContingencyState[]> scheme
public static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] NA
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] EMPTY
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_ONLY
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_ONLY
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TN_ONLY
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FN_ONLY
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FP
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_TN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_FN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_TN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] FP_TN_FN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TP_FP_FN
protected static final picard.vcf.GenotypeConcordanceStates.ContingencyState[] TN_FN
protected abstract void initiateScheme()
protected void addRow(picard.vcf.GenotypeConcordanceStates.CallState callState, picard.vcf.GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
callState
- the call state (row)concordanceStateArrays
- the concordance state arrays for each truth value, in orderpublic picard.vcf.GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState)
public picard.vcf.GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(picard.vcf.GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
public String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, picard.vcf.GenotypeConcordanceStates.CallState callState)
public Set<picard.vcf.GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(picard.vcf.GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)
contingencyStateArray
- public void validateScheme() throws PicardException
PicardException
- if a missing tuple was found.