htsjdk.samtools.cram.ref

Class CRAMLazyReferenceSource

java.lang.Object

htsjdk.samtools.cram.ref.CRAMLazyReferenceSource

All Implemented Interfaces:

CRAMReferenceSource

public class CRAMLazyReferenceSource
extends java.lang.Object
implements CRAMReferenceSource

A lazy CRAMReferenceSource implementation, for use when no explicit reference source has been provided by the user. This allows client code to have a CRAMReferenceSource to thread through the CRAM code and to access containers, slices, and un-normalized CRAM records and otherwise perform operations such as indexing that do not require a reference to be resolved. If a reference sequence is actually requested, throws an exception.

Constructor Summary

Constructors

Constructor and Description
CRAMLazyReferenceSource()

Method Summary

Modifier and Type	Method and Description
byte[]	getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants) getReferenceBases

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CRAMLazyReferenceSource

public CRAMLazyReferenceSource()

Method Detail

getReferenceBases

public byte[] getReferenceBases(SAMSequenceRecord sequenceRecord,
                                boolean tryNameVariants)

Description copied from interface: CRAMReferenceSource

getReferenceBases

Specified by:

getReferenceBases in interface CRAMReferenceSource

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