OverclippedReadFilter (htsjdk 2.24.1 API)

java.lang.Object
- htsjdk.samtools.filter.OverclippedReadFilter

All Implemented Interfaces:

SamRecordFilter
```
public class OverclippedReadFilter
extends Object
implements SamRecordFilter
```
Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g. bacterial contamination. Based on GATK's OverclippedReadFilter.

Constructor Summary

Constructors
Constructor Description

OverclippedReadFilter(int unclippedBasesThreshold, boolean filterSingleEndClips)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`filterOut(SAMRecord record)`	Determines whether a SAMRecord matches this filter
`boolean`	`filterOut(SAMRecord first, SAMRecord second)`	Determines whether a pair of SAMRecords matches this filter

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

- Constructor Detail
  - OverclippedReadFilter
```
public OverclippedReadFilter(int unclippedBasesThreshold,
                             boolean filterSingleEndClips)
```
- Method Detail
  - filterOut
```
public boolean filterOut(SAMRecord record)
```
    Description copied from interface: SamRecordFilter
    
    Determines whether a SAMRecord matches this filter
    
    Specified by:
    
    filterOut in interface SamRecordFilter
    
    Parameters:
    
    record - the SAMRecord to evaluate
    
    Returns:
    
    true if the SAMRecord matches the filter, otherwise false
  - filterOut
```
public boolean filterOut(SAMRecord first,
                         SAMRecord second)
```
    Description copied from interface: SamRecordFilter
    
    Determines whether a pair of SAMRecords matches this filter
    
    Specified by:
    
    filterOut in interface SamRecordFilter
    
    Parameters:
    
    first - the first SAMRecord to evaluate
    
    second - the second SAMRecord to evaluate
    
    Returns:
    
    true if the pair of records matches filter, otherwise false