CRAMReferenceSource (htsjdk 2.18.2 API)

All Known Implementing Classes:

ReferenceSource
```
public interface CRAMReferenceSource
```
Interface used to supply a reference source when reading CRAM files.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`byte[]`	`getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants)`	getReferenceBases

- Method Detail
  - getReferenceBases
```
byte[] getReferenceBases(SAMSequenceRecord sequenceRecord,
                         boolean tryNameVariants)
```
    getReferenceBases
    
    Parameters:
    
    sequenceRecord - the SAMSequenceRecord identifying the reference being requested
    
    tryNameVariants - 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 match
    
    Returns:
    
    the upper cased, normalized (see Utils.normalizeBase(byte)) bases representing the requested sequence, or null if the sequence cannot be found