Package picard.sam.SamErrorMetric
Class BaseErrorMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.BaseErrorMetric
- Direct Known Subclasses:
IndelErrorMetric
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class BaseErrorMetric
extends ErrorMetric
An error metric for the errors in bases.
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Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
The number of bases that disagree with the referenceint
The (phred) rate of bases that disagree with the referenceFields inherited from class picard.sam.SamErrorMetric.ErrorMetric
COVARIATE, PRIOR_ERROR, TOTAL_BASES
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.Methods inherited from class picard.sam.SamErrorMetric.ErrorMetric
computeQScore, computeQScore, setPriorError
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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ERROR_BASES
public long ERROR_BASESThe number of bases that disagree with the reference -
Q_SCORE
public int Q_SCOREThe (phred) rate of bases that disagree with the reference
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Constructor Details
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BaseErrorMetric
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BaseErrorMetric
public BaseErrorMetric()
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Method Details
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calculateDerivedFields
public void calculateDerivedFields()Description copied from class:MergeableMetricBase
Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated withNoMergingKeepsValue
.- Overrides:
calculateDerivedFields
in classMergeableMetricBase
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