Package picard.analysis.artifacts
Class ErrorSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.artifacts.ErrorSummaryMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class ErrorSummaryMetrics
extends MergeableMetricBase
Summary metrics produced by
CollectSequencingArtifactMetrics
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.-
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 TypeFieldDescriptionchar
The alternative base (or it's complement).long
The number of alt bases observed.char
The reference base (or it's complement).long
The number of reference bases observed.A single string representing the substition from REF_BASE to ALT_BASE for convenience.double
The rate of the substitution in question. -
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.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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REF_BASE
public char REF_BASEThe reference base (or it's complement). -
ALT_BASE
public char ALT_BASEThe alternative base (or it's complement). -
SUBSTITUTION
A single string representing the substition from REF_BASE to ALT_BASE for convenience. -
REF_COUNT
public long REF_COUNTThe number of reference bases observed. -
ALT_COUNT
public long ALT_COUNTThe number of alt bases observed. -
SUBSTITUTION_RATE
public double SUBSTITUTION_RATEThe rate of the substitution in question.
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Constructor Details
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ErrorSummaryMetrics
public ErrorSummaryMetrics()
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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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