htsjdk.samtools

Class HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter

java.lang.Object

htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter

All Implemented Interfaces:

SamRecordFilter

Enclosing class:

HtsgetBAMFileReader

public static class HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter
extends java.lang.Object
implements SamRecordFilter

Filters out records that do not match any of the given intervals and query type.

Constructor Summary

Constructors

Constructor and Description
BAMQueryMultipleIntervalsIteratorFilter(java.util.List<Locatable> intervals, boolean contained)

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

BAMQueryMultipleIntervalsIteratorFilter

public BAMQueryMultipleIntervalsIteratorFilter(java.util.List<Locatable> intervals,
                                               boolean contained)

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