Package htsjdk.samtools.util

Class SamLocusIterator.LocusInfo

java.lang.Object

htsjdk.samtools.util.AbstractLocusInfo<SamLocusIterator.RecordAndOffset>

htsjdk.samtools.util.SamLocusIterator.LocusInfo

All Implemented Interfaces:

Locatable, Locus

Enclosing class:

SamLocusIterator

public static final class SamLocusIterator.LocusInfo
extends AbstractLocusInfo<SamLocusIterator.RecordAndOffset>

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; two more List_s_ of ReadAndOffset objects include reads that overlap the locus with insertions and deletions respectively

Constructor Summary

Constructors

Constructor	Description
LocusInfo(SAMSequenceRecord referenceSequence, int position)

Method Summary

Modifier and Type	Method	Description
void	addDeleted(SAMRecord read, int previousPosition)	Accumulate info for one read with a deletion
void	addInserted(SAMRecord read, int firstPosition)	Accumulate info for one read with an insertion.
List<SamLocusIterator.RecordAndOffset>	getDeletedInRecord()
List<SamLocusIterator.RecordAndOffset>	getInsertedInRecord()
boolean	isEmpty()
int	size()

Methods inherited from class htsjdk.samtools.util.AbstractLocusInfo

add, getContig, getEnd, getPosition, getRecordAndOffsets, getRecordAndPositions, getSequenceIndex, getSequenceLength, getSequenceName, getStart, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Details

LocusInfo

public LocusInfo(SAMSequenceRecord referenceSequence,
 int position)

Parameters:

referenceSequence - reference sequence at which the reads are aligned

position - position in the sequence at which the reads are aligned

Method Details

addDeleted

public void addDeleted(SAMRecord read,
 int previousPosition)

Accumulate info for one read with a deletion

addInserted

public void addInserted(SAMRecord read,
 int firstPosition)

Accumulate info for one read with an insertion. For this locus, the reads in the insertion are included also in recordAndOffsets

getDeletedInRecord

public List<SamLocusIterator.RecordAndOffset> getDeletedInRecord()

getInsertedInRecord

public List<SamLocusIterator.RecordAndOffset> getInsertedInRecord()

size

public int size()

Overrides:

size in class AbstractLocusInfo<SamLocusIterator.RecordAndOffset>

Returns:

the number of records overlapping the position, with deletions included if they are being tracked.

isEmpty

public boolean isEmpty()

Overrides:

isEmpty in class AbstractLocusInfo<SamLocusIterator.RecordAndOffset>

Returns:

true if all the RecordAndOffset lists are empty; false if at least one have records