Package picard.analysis.artifacts
Class ErrorSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.analysis.artifacts.ErrorSummaryMetrics
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@DocumentedFeature(groupName="Metrics", summary="Metrics") public class ErrorSummaryMetrics extends MergeableMetricBase
Summary metrics produced byCollectSequencingArtifactMetrics
as a roll up of the context-specific error rates, to provide global error rates per type of base substitution. Errors are normalized to the lexically lower reference base and summarized together. E.g. G>T is converted to C>A and merged with data from C>A for reporting.
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Nested Class Summary
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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
Fields Modifier and Type Field Description char
ALT_BASE
The alternative base (or it's complement).long
ALT_COUNT
The number of alt bases observed.char
REF_BASE
The reference base (or it's complement).long
REF_COUNT
The number of reference bases observed.String
SUBSTITUTION
A single string representing the substition from REF_BASE to ALT_BASE for convenience.double
SUBSTITUTION_RATE
The rate of the substitution in question.
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Constructor Summary
Constructors Constructor Description ErrorSummaryMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calculateDerivedFields()
Placeholder method that will calculate the derived fields from the other ones.-
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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REF_BASE
public char REF_BASE
The reference base (or it's complement).
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ALT_BASE
public char ALT_BASE
The alternative base (or it's complement).
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SUBSTITUTION
public String SUBSTITUTION
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
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REF_COUNT
public long REF_COUNT
The number of reference bases observed.
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ALT_COUNT
public long ALT_COUNT
The number of alt bases observed.
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SUBSTITUTION_RATE
public double SUBSTITUTION_RATE
The rate of the substitution in question.
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Method Detail
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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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