htsjdk.samtools.util

Class SamLocusIterator.LocusInfo

java.lang.Object

htsjdk.samtools.util.SamLocusIterator.LocusInfo

All Implemented Interfaces:

Locus

Enclosing class:

SamLocusIterator

public static final class SamLocusIterator.LocusInfo
extends java.lang.Object
implements Locus

The unit of iteration. Holds information about the locus (the SAMSequenceRecord and 1-based position on the reference), plus List of ReadAndOffset objects, one for each read that overlaps the locus

Method Summary

Modifier and Type	Method and Description
void	add(SAMRecord read, int position) Accumulate info for one read at the locus.
int	getPosition()
java.util.List<SamLocusIterator.RecordAndOffset>	getRecordAndPositions()
int	getSequenceIndex()
int	getSequenceLength()
java.lang.String	getSequenceName()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

add

public void add(SAMRecord read,
                int position)

Accumulate info for one read at the locus.

getSequenceIndex

public int getSequenceIndex()

Specified by:

getSequenceIndex in interface Locus

getPosition

public int getPosition()

Specified by:

getPosition in interface Locus

Returns:

1-based reference position

getRecordAndPositions

public java.util.List<SamLocusIterator.RecordAndOffset> getRecordAndPositions()

getSequenceName

public java.lang.String getSequenceName()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getSequenceLength

public int getSequenceLength()