htsjdk.samtools.cram.ref

Interface CRAMReferenceSource

All Known Implementing Classes:

ReferenceSource

public interface CRAMReferenceSource

Interface used to supply a reference source when reading CRAM files.

Method Summary

Modifier and Type	Method and 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