Package htsjdk.samtools.cram.ref

Class CRAMLazyReferenceSource

java.lang.Object

htsjdk.samtools.cram.ref.CRAMLazyReferenceSource

All Implemented Interfaces:

CRAMReferenceSource

public class CRAMLazyReferenceSource
extends 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	Description
CRAMLazyReferenceSource()

Method Summary

Modifier and Type	Method	Description
byte[]	getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants)	Get the reference bases for an entire reference contig.
byte[]	getReferenceBasesByRegion(SAMSequenceRecord sequenceRecord, int zeroBasedStart, int requestedRegionLength)	Get the reference bases for a region of a reference contig.

Methods inherited from class java.lang.Object

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

Constructor Details

CRAMLazyReferenceSource

public CRAMLazyReferenceSource()

Method Details

getReferenceBases

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

Description copied from interface: CRAMReferenceSource

Get the reference bases for an entire reference contig.

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

getReferenceBasesByRegion

public byte[] getReferenceBasesByRegion(SAMSequenceRecord sequenceRecord,
 int zeroBasedStart,
 int requestedRegionLength)

Description copied from interface: CRAMReferenceSource

Get the reference bases for a region of a reference contig. If the sequence can be retrieved, but is not long enough to satisfy the requested length, it is permissible to return fewer bases than the requestedRegionLength. It is the caller's responsibility to detect and handle this case.

Specified by:

getReferenceBasesByRegion in interface CRAMReferenceSource

Parameters:

sequenceRecord - the SAMSequenceRecord for the reference contig being requested

zeroBasedStart - the zero based offset of the starting reference base, must be >= 0

requestedRegionLength - the length of the requested reference region

Returns:

the bases for the reference region, or null if the sequence cannot be found.