SecondaryAlignmentFilter (htsjdk 2.14.3 API)

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

All Implemented Interfaces:

SamRecordFilter

Direct Known Subclasses:

NotPrimaryAlignmentFilter
```
public class SecondaryAlignmentFilter
extends Object
implements SamRecordFilter
```
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.

Constructor Summary

Constructors
Constructor Description

SecondaryAlignmentFilter()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`filterOut(SAMRecord record)`	Returns true if the read is marked as secondary.
`boolean`	`filterOut(SAMRecord first, SAMRecord second)`	Returns true if either read is marked as secondary.

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

- Constructor Detail
  - SecondaryAlignmentFilter
```
public SecondaryAlignmentFilter()
```
- Method Detail
  - filterOut
```
public boolean filterOut(SAMRecord record)
```
    Returns true if the read is marked as secondary.
    
    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)
```
    Returns true if either read is marked as secondary.
    
    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

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