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 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.