public interface CRAMReferenceSource
Modifier and Type | Method and Description |
---|---|
byte[] |
getReferenceBases(SAMSequenceRecord sequenceRecord,
boolean tryNameVariants)
getReferenceBases
|
byte[] getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants)
sequenceRecord
- the SAMSequenceRecord identifying the reference
being requestedtryNameVariants
- if true, attempt to match the requested sequence name
against the reference by using common name variations,
such as adding or removing a leading "chr" prefix
from the requested name. if false, use exact matchUtils.normalizeBase(byte)
)
bases representing the requested sequence, or null if the sequence cannot be found