htsjdk.samtools

Class BAMQueryMultipleIntervalsIteratorFilter

java.lang.Object

htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter

public class BAMQueryMultipleIntervalsIteratorFilter
extends java.lang.Object

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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	htsjdk.samtools.BAMIteratorFilter.FilteringIteratorState Type returned by BAMIteratorFilter that tell iterators implementing this interface how to handle each SAMRecord.
static class	htsjdk.samtools.BAMIteratorFilter.IntervalComparison

Constructor Summary

Constructors

Constructor and Description
BAMQueryMultipleIntervalsIteratorFilter(QueryInterval[] intervals, boolean contained)

Method Summary

Modifier and Type	Method and Description
static htsjdk.samtools.BAMIteratorFilter.IntervalComparison	compareIntervalToRecord(QueryInterval interval, SAMRecord record)
htsjdk.samtools.BAMIteratorFilter.FilteringIteratorState	compareToFilter(SAMRecord record) Determine if given record passes the filter, and if it does not, whether iteration should continue or if this record is beyond the region(s) of interest.

Methods inherited from class java.lang.Object

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

Constructor Detail

BAMQueryMultipleIntervalsIteratorFilter

public BAMQueryMultipleIntervalsIteratorFilter(QueryInterval[] intervals,
                                               boolean contained)

Method Detail

compareToFilter

public htsjdk.samtools.BAMIteratorFilter.FilteringIteratorState compareToFilter(SAMRecord record)

Determine if given record passes the filter, and if it does not, whether iteration should continue or if this record is beyond the region(s) of interest.

compareIntervalToRecord

public static htsjdk.samtools.BAMIteratorFilter.IntervalComparison compareIntervalToRecord(QueryInterval interval,
                                                                                           SAMRecord record)