htsjdk.samtools.filter

Class SolexaNoiseFilter

java.lang.Object

htsjdk.samtools.filter.SolexaNoiseFilter

All Implemented Interfaces:

SamRecordFilter

public class SolexaNoiseFilter
extends java.lang.Object
implements SamRecordFilter

Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact. Currently we filter out only reads that are composed entirely of As. $Id$

Constructor Summary

Constructors

Constructor and Description
SolexaNoiseFilter()

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

SolexaNoiseFilter

public SolexaNoiseFilter()

Method Detail

filterOut

public boolean filterOut(SAMRecord record)

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