IndelErrorCalculator (picard 2.26.10 API)

java.lang.Object
- picard.sam.SamErrorMetric.BaseErrorCalculator
- - picard.sam.SamErrorMetric.IndelErrorCalculator

All Implemented Interfaces:

BaseCalculator
```
public class IndelErrorCalculator
extends BaseErrorCalculator
```
A calculator that estimates the error rate of the bases it observes for indels only.

Field Summary

Fields
Modifier and Type	Field	Description
`protected long`	`nDeletedBases`	Total number of deleted bases
`protected long`	`nDeletions`	Total number of deletions
`protected long`	`nInsertedBases`	Total number of inserted bases
`protected long`	`nInsertions`	Total number of inserts

Constructor Summary

Constructors
Constructor Description

IndelErrorCalculator()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)`	the function by which new loci are "shown" to the calculator
`IndelErrorMetric`	`getMetric()`	Returns the metric generated by the observed loci
`String`	`getSuffix()`	The suffix that pertains to the implementation of aggregation

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - nInsertions
```
protected long nInsertions
```
    Total number of inserts
  - nInsertedBases
```
protected long nInsertedBases
```
    Total number of inserted bases
  - nDeletions
```
protected long nDeletions
```
    Total number of deletions
  - nDeletedBases
```
protected long nDeletedBases
```
    Total number of deleted bases
- Constructor Detail
  - IndelErrorCalculator
```
public IndelErrorCalculator()
```
- Method Detail
  - addBase
```
public void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset,
                    htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
```
    Description copied from class: BaseErrorCalculator
    
    the function by which new loci are "shown" to the calculator
    
    Specified by:
    
    addBase in interface BaseCalculator
    
    Overrides:
    
    addBase in class BaseErrorCalculator
  - getSuffix
```
public String getSuffix()
```
    The suffix that pertains to the implementation of aggregation
  - getMetric
```
public IndelErrorMetric getMetric()
```
    Returns the metric generated by the observed loci