htsjdk.samtools.filter

Class ReadNameFilter

java.lang.Object

htsjdk.samtools.filter.ReadNameFilter

All Implemented Interfaces:

SamRecordFilter

public class ReadNameFilter
extends java.lang.Object
implements SamRecordFilter

Filter by a set of specified readnames

$Id$

Constructor Summary

Constructors

Constructor and Description
ReadNameFilter(java.io.File readNameFilterFile, boolean includeReads)
ReadNameFilter(java.util.Set<java.lang.String> readNameFilterSet, boolean includeReads)

Method Summary

Methods

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

ReadNameFilter

public ReadNameFilter(java.io.File readNameFilterFile,
              boolean includeReads)

ReadNameFilter

public ReadNameFilter(java.util.Set<java.lang.String> readNameFilterSet,
              boolean includeReads)

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 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