Package htsjdk.samtools.filter

Class SecondaryAlignmentFilter

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

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 Details

SecondaryAlignmentFilter

public SecondaryAlignmentFilter()

Method Details

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