htsjdk.samtools

Class BAMStartingAtIteratorFilter

java.lang.Object

htsjdk.samtools.BAMStartingAtIteratorFilter

public class BAMStartingAtIteratorFilter
extends java.lang.Object

A decorating iterator that filters out records that do not match the given reference and start position.

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
BAMStartingAtIteratorFilter(int referenceIndex, int start)

Method Summary

Modifier and Type	Method and Description
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

BAMStartingAtIteratorFilter

public BAMStartingAtIteratorFilter(int referenceIndex,
                                   int start)

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.

Returns:

MATCHES_FILTER if this record matches the filter; CONTINUE_ITERATION if does not match filter but iteration should continue; STOP_ITERATION if does not match filter and iteration should end.