htsjdk.samtools.filter

Class IntervalFilter

java.lang.Object

htsjdk.samtools.filter.IntervalFilter

All Implemented Interfaces:

SamRecordFilter

public class IntervalFilter
extends java.lang.Object
implements SamRecordFilter

Filter SAMRecords so that only those that overlap the given list of intervals. It is required that the SAMRecords are passed in coordinate order, and have non-null SAMFileHeaders. $Id$

Constructor Summary

Constructors

Constructor and Description
IntervalFilter(java.util.List<Interval> intervals, SAMFileHeader samHeader) Prepare to filter out SAMRecords that do not overlap the given list of intervals

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

IntervalFilter

public IntervalFilter(java.util.List<Interval> intervals,
                      SAMFileHeader samHeader)

Prepare to filter out SAMRecords that do not overlap the given list of intervals

Parameters:

intervals - -- must be locus-ordered & non-overlapping

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