public abstract class EdgingRecordAndOffset extends AbstractRecordAndOffset
type
added to indicate whether object
represents the start or the end of an alignment block.
Subclasses StartEdgingRecordAndOffset and EndEdgingRecordAndOffset are used in EdgeReadIterator to
distinguish starting and ending of the alignment block
as for each alignment block two objects of EdgingRecordAndOffset
are created with two different types.
The main idea of using EdgeReadIterator is to process alignment block starting from locus where BEGIN type occurs,
aggregate information per locus and keep it until END type occurs, then remove alignment block from consideration.
Modifier and Type | Class and Description |
---|---|
static class |
EdgingRecordAndOffset.Type
Describes the type of
TypedRecordAndOffset , whether it represents the start or the end of
an alignment block. |
offset, record
Modifier and Type | Method and Description |
---|---|
static EdgingRecordAndOffset |
createBeginRecord(SAMRecord record,
int offset,
int length,
int refPos) |
static EdgingRecordAndOffset |
createEndRecord(EdgingRecordAndOffset startRecord) |
abstract byte |
getBaseQuality(int position) |
abstract int |
getRefPos() |
abstract EdgingRecordAndOffset |
getStart() |
abstract EdgingRecordAndOffset.Type |
getType() |
getBaseQualities, getBaseQuality, getLength, getOffset, getReadBase, getReadName, getRecord, validateOffset
public abstract EdgingRecordAndOffset getStart()
public abstract EdgingRecordAndOffset.Type getType()
public abstract byte getBaseQuality(int position)
public abstract int getRefPos()
public static EdgingRecordAndOffset createBeginRecord(SAMRecord record, int offset, int length, int refPos)
public static EdgingRecordAndOffset createEndRecord(EdgingRecordAndOffset startRecord)