htsjdk.samtools.cram.ref

Interface CRAMReferenceSource

All Known Implementing Classes:

CRAMLazyReferenceSource, 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) 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.

Method Detail

getReferenceBases

byte[] getReferenceBases(SAMSequenceRecord sequenceRecord,
                         boolean tryNameVariants)

Get the reference bases for an entire reference contig.

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

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

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.

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.