Interface CRAMReferenceSource

    • 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