public static final class SamLocusIterator.LocusInfo extends AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
| Constructor and Description |
|---|
LocusInfo(SAMSequenceRecord referenceSequence,
int position) |
| Modifier and Type | Method and 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.
|
java.util.List<SamLocusIterator.RecordAndOffset> |
getDeletedInRecord() |
java.util.List<SamLocusIterator.RecordAndOffset> |
getInsertedInRecord() |
boolean |
isEmpty() |
int |
size() |
add, getContig, getEnd, getPosition, getRecordAndOffsets, getRecordAndPositions, getSequenceIndex, getSequenceLength, getSequenceName, getStart, toStringclone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitcontains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOfpublic 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 java.util.List<SamLocusIterator.RecordAndOffset> getDeletedInRecord()
public java.util.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