picard.analysis.artifacts

Class ErrorSummaryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.MergeableMetricBase

picard.analysis.artifacts.ErrorSummaryMetrics

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

Field Summary

Fields

Modifier and Type	Field and 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.
java.lang.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.

Constructor Summary

Constructors

Constructor and Description
ErrorSummaryMetrics()

Method Summary

Modifier and Type	Method and 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

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

REF_BASE

public char REF_BASE

The reference base (or it's complement).

ALT_BASE

public char ALT_BASE

The alternative base (or it's complement).

SUBSTITUTION

public java.lang.String SUBSTITUTION

A single string representing the substition from REF_BASE to ALT_BASE for convenience.

REF_COUNT

public long REF_COUNT

The number of reference bases observed.

ALT_COUNT

public long ALT_COUNT

The number of alt bases observed.

SUBSTITUTION_RATE

public double SUBSTITUTION_RATE

The rate of the substitution in question.

Constructor Detail

ErrorSummaryMetrics

public ErrorSummaryMetrics()

Method Detail

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 with NoMergingKeepsValue.

Overrides:

calculateDerivedFields in class MergeableMetricBase