Package picard.sam.SamErrorMetric
Class IndelErrorMetric
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.sam.SamErrorMetric.ErrorMetric
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- picard.sam.SamErrorMetric.BaseErrorMetric
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- picard.sam.SamErrorMetric.IndelErrorMetric
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public class IndelErrorMetric extends BaseErrorMetric
Metric to be used for InDel errors
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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 int
DELETIONS_Q
The (phred) rate of deletions.int
INSERTIONS_Q
The (phred) rate of insertions.long
NUM_DELETED_BASES
The number of deleted bases.long
NUM_DELETIONS
The number of deletions.long
NUM_INSERTED_BASES
The number of inserted bases.long
NUM_INSERTIONS
The number of insertions.-
Fields inherited from class picard.sam.SamErrorMetric.BaseErrorMetric
ERROR_BASES, Q_SCORE
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Fields inherited from class picard.sam.SamErrorMetric.ErrorMetric
COVARIATE, PRIOR_ERROR, TOTAL_BASES
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Constructor Summary
Constructors Constructor Description IndelErrorMetric()
IndelErrorMetric(String covariate, long nTotalBases, long nInserts, long nInsertedBases, long nDeletions, long nDeletedBases)
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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.sam.SamErrorMetric.ErrorMetric
computeQScore, computeQScore, setPriorError
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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NUM_INSERTIONS
public long NUM_INSERTIONS
The number of insertions. Note: This is not the number of bases that have been inserted.
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NUM_INSERTED_BASES
public long NUM_INSERTED_BASES
The number of inserted bases.
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INSERTIONS_Q
public int INSERTIONS_Q
The (phred) rate of insertions.
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NUM_DELETIONS
public long NUM_DELETIONS
The number of deletions. Note: This is not the number of bases that have been deleted.
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NUM_DELETED_BASES
public long NUM_DELETED_BASES
The number of deleted bases.
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DELETIONS_Q
public int DELETIONS_Q
The (phred) rate of deletions.
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Constructor Detail
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IndelErrorMetric
public IndelErrorMetric(String covariate, long nTotalBases, long nInserts, long nInsertedBases, long nDeletions, long nDeletedBases)
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IndelErrorMetric
public IndelErrorMetric()
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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 classBaseErrorMetric
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