SecondaryOrSupplementaryFilter (htsjdk 2.24.1 API)

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

All Implemented Interfaces:

SamRecordFilter
```
public class SecondaryOrSupplementaryFilter
extends Object
implements SamRecordFilter
```
Filter out SAMRecords with Secondary or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator, in that we did not want to change the functionality of NPSI to no longer match its name $Id$

Constructor Summary

Constructors
Constructor Description

SecondaryOrSupplementaryFilter()

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 SAMRecord matches this filter

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

- Constructor Detail
  - SecondaryOrSupplementaryFilter
```
public SecondaryOrSupplementaryFilter()
```
- 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)
```
    Determines whether a pair of SAMRecord 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 SAMRecords matches the filter, otherwise false