Package picard.sam.SamErrorMetric
Class IndelErrorMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.BaseErrorMetric
picard.sam.SamErrorMetric.IndelErrorMetric
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class IndelErrorMetric
extends BaseErrorMetric
Metric to be used for InDel errors
-
Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
-
Field Summary
FieldsModifier and TypeFieldDescriptionint
The (phred) rate of deletions.int
The (phred) rate of insertions.long
The number of deleted bases.long
The number of deletions.long
The number of inserted bases.long
The number of insertions.Fields inherited from class picard.sam.SamErrorMetric.BaseErrorMetric
ERROR_BASES, Q_SCORE
Fields inherited from class picard.sam.SamErrorMetric.ErrorMetric
COVARIATE, PRIOR_ERROR, TOTAL_BASES
-
Constructor Summary
ConstructorsConstructorDescriptionIndelErrorMetric
(String covariate, long nTotalBases, long nInserts, long nInsertedBases, long nDeletions, long nDeletedBases) -
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
-
Field Details
-
NUM_INSERTIONS
public long NUM_INSERTIONSThe number of insertions. Note: This is not the number of bases that have been inserted. -
NUM_INSERTED_BASES
public long NUM_INSERTED_BASESThe number of inserted bases. -
INSERTIONS_Q
public int INSERTIONS_QThe (phred) rate of insertions. -
NUM_DELETIONS
public long NUM_DELETIONSThe number of deletions. Note: This is not the number of bases that have been deleted. -
NUM_DELETED_BASES
public long NUM_DELETED_BASESThe number of deleted bases. -
DELETIONS_Q
public int DELETIONS_QThe (phred) rate of deletions.
-
-
Constructor Details
-
IndelErrorMetric
public IndelErrorMetric(String covariate, long nTotalBases, long nInserts, long nInsertedBases, long nDeletions, long nDeletedBases) -
IndelErrorMetric
public IndelErrorMetric()
-
-
Method Details
-
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 classBaseErrorMetric
-