Locus
public static final class SamLocusIterator.LocusInfo extends AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
Constructor | Description |
---|---|
LocusInfo(SAMSequenceRecord referenceSequence,
int position) |
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() |
add, getPosition, getRecordAndOffsets, getRecordAndPositions, getSequenceIndex, getSequenceLength, getSequenceName, toString
public LocusInfo(SAMSequenceRecord referenceSequence, int position)
referenceSequence
- reference sequence at which the reads are alignedposition
- position in the sequence at which the reads are alignedpublic void addDeleted(SAMRecord read, int previousPosition)
public void addInserted(SAMRecord read, int firstPosition)
public List<SamLocusIterator.RecordAndOffset> getDeletedInRecord()
public List<SamLocusIterator.RecordAndOffset> getInsertedInRecord()
public int size()
size
in class AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
public boolean isEmpty()
isEmpty
in class AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
true
if all the RecordAndOffset lists are empty;
false
if at least one have records