ErrorMetric (picard 2.18.25 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.MergeableMetricBase
  - - picard.sam.SamErrorMetric.ErrorMetric

Direct Known Subclasses:

BaseErrorMetric, OverlappingErrorMetric
```
public class ErrorMetric
extends MergeableMetricBase
```
Created by farjoun on 6/26/18.

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	Description
`String`	`COVARIATE`	The value of the covariate define the bases included in this metric
`protected static double`	`PRIOR_ERROR`
`long`	`TOTAL_BASES`	The total number of bases included in the calculation of this metric

Constructor Summary

Constructors
Constructor Description

ErrorMetric()

ErrorMetric(String covariate, long totalBases)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`computeQScore(long numberOfErrors)`	compute a qscore given the number of errors and the total number of bases.
`protected int`	`computeQScore(long numberOfErrors, long nTotalBases)`	compute a qscore given the number of errors and the total number of bases.
`static void`	`setPriorError(double priorError)`

Methods inherited from class picard.analysis.MergeableMetricBase
calculateDerivedFields, 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
  - PRIOR_ERROR
```
protected static double PRIOR_ERROR
```
  - COVARIATE
```
public String COVARIATE
```
    The value of the covariate define the bases included in this metric
  - TOTAL_BASES
```
public long TOTAL_BASES
```
    The total number of bases included in the calculation of this metric
- Constructor Detail
  - ErrorMetric
```
public ErrorMetric(String covariate,
                   long totalBases)
```
  - ErrorMetric
```
public ErrorMetric()
```
- Method Detail
  - setPriorError
```
public static void setPriorError(double priorError)
```
  - computeQScore
```
protected int computeQScore(long numberOfErrors)
```
    compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the numerator and 1/PRIOR_ERROR in the denominator.
  - computeQScore
```
protected int computeQScore(long numberOfErrors,
                            long nTotalBases)
```
    compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the denominator and 1 in the numerator.