htsjdk.samtools.filter

Class OverclippedReadFilter

java.lang.Object

htsjdk.samtools.filter.OverclippedReadFilter

All Implemented Interfaces:

SamRecordFilter

public class OverclippedReadFilter
extends java.lang.Object
implements SamRecordFilter

Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g. bacterial contamination. Based on GATK's OverclippedReadFilter.

Constructor Summary

Constructors

Constructor and Description
OverclippedReadFilter(int unclippedBasesThreshold, boolean filterSingleEndClips)

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 SAMRecords matches this filter

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OverclippedReadFilter

public OverclippedReadFilter(int unclippedBasesThreshold,
                             boolean filterSingleEndClips)

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)

Description copied from interface: SamRecordFilter

Determines whether a pair of SAMRecords 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 pair of records matches filter, otherwise false