htsjdk.samtools.filter

Class SecondaryOrSupplementaryFilter

java.lang.Object

htsjdk.samtools.filter.SecondaryOrSupplementaryFilter

All Implemented Interfaces:

SamRecordFilter

public class SecondaryOrSupplementaryFilter
extends java.lang.Object
implements SamRecordFilter

Filter out SAMRecords with NotPrimaryAlignment 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 and Description
SecondaryOrSupplementaryFilter()

Method Summary

Modifier and Type	Method and 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