public static final class SamLocusIterator.LocusInfo extends java.lang.Object implements Locus
Modifier and Type | Method and Description |
---|---|
void |
add(SAMRecord read,
int position)
Accumulate info for one read at the locus.
|
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() |
int |
getPosition() |
java.util.List<SamLocusIterator.RecordAndOffset> |
getRecordAndPositions() |
int |
getSequenceIndex() |
int |
getSequenceLength() |
java.lang.String |
getSequenceName() |
boolean |
isEmpty() |
java.lang.String |
toString() |
public void add(SAMRecord read, int position)
public void addDeleted(SAMRecord read, int previousPosition)
public void addInserted(SAMRecord read, int firstPosition)
public int getSequenceIndex()
getSequenceIndex
in interface Locus
public int getPosition()
getPosition
in interface Locus
public java.util.List<SamLocusIterator.RecordAndOffset> getRecordAndPositions()
public java.lang.String getSequenceName()
public java.lang.String toString()
toString
in class java.lang.Object
public int getSequenceLength()
public java.util.List<SamLocusIterator.RecordAndOffset> getDeletedInRecord()
public java.util.List<SamLocusIterator.RecordAndOffset> getInsertedInRecord()
public boolean isEmpty()
true
if all the RecordAndOffset lists are empty;
false
if at least one have records