Package htsjdk.samtools.cram.build

Class CRAMReferenceRegion

java.lang.Object
htsjdk.samtools.cram.build.CRAMReferenceRegion
public class CRAMReferenceRegion extends Object
Holds a region/fragment of a reference contig. Maintains a CRAMReferenceSource for retrieving additional regions. This is a mutable object that is used to traverse along a reference contig via serial calls to either fetchReferenceBases(int) or fetchReferenceBasesByRegion(int, int, int). It caches the bases from the previous request, along with metadata about the (0-based) start offset, and length of the cached bases. NOTE: this class is not thread-safe/safe for concurrent access across threads.

  • Field Details

  • Constructor Details

  • Method Details

    • getCurrentReferenceBases

      public byte[] getCurrentReferenceBases()
      Returns:
      the currently cached reference bases (may return null)

    • getReferenceIndex

      public int getReferenceIndex()
      Returns:
      the current reference index or ReferenceContext.UNINITIALIZED_REFERENCE_ID if no index has been established

    • getRegionStart

      public int getRegionStart()
      Returns:
      the 0-based start position of the range of the current reference sequence region. UNINITIALIZED_START if no region has been established

    • getRegionLength

      public int getRegionLength()
      Returns:
      the length of the current reference sequence region. UNINITIALIZED_LENGTH if no region has been established

    • fetchReferenceBases

      public void fetchReferenceBases(int referenceIndex)
      Return the reference bases for an entire contig given a reference contig index. Note: Serial calls to this method on behalf of non-coordinate sorted inputs can result in thrashing and poor performance due to repeated calls to the underlying CRAMReferenceSource, especially when the CRAMReferenceSource is fetching bases from a remote reference.
      Parameters:
      referenceIndex - the reference index for which bases should be retrieved.
      Throws:
      IllegalArgumentException - if the requested index is not present in the sequence dictionary or if the sequence's bases cannot be retrieved from the CRAMReferenceSource

    • fetchReferenceBasesByRegion

      public void fetchReferenceBasesByRegion(int referenceIndex, int zeroBasedStart, int requestedFragmentLength)
      Get the reference bases for a region of a reference contig. If the current region does not match the requested region, the referenceSource will be called to retrieve the bases. The caller cannot assume that the entire region requested is always fetched (if the requested range matches the alignment span for CRAM record or slice contains a CRAM records that is mapped beyond the end of the reference contig, fewer bases than were requested may be fetched.
      Parameters:
      referenceIndex - reference index for which to retrieve bases
      zeroBasedStart - zero based start of the first base to be retrieved
      requestedFragmentLength - length of the fragment to be retrieved
      Throws:
      IllegalArgumentException - if the requested sequence cannot be located in the sequence dictionary, or if the requested sequence cannot be provided by the underlying referenceSource

    • fetchReferenceBasesByRegion

      public void fetchReferenceBasesByRegion(AlignmentContext alignmentContext)
      Fetch the bases to span an AlignmentContext.
      Parameters:
      alignmentContext - the alignment context for which to fetch bases. must be an AlignmentContext for a single reference ReferenceContextType.SINGLE_REFERENCE_TYPE slice (see ReferenceContext.isMappedSingleRef())

    • setEmbeddedReferenceBases

      public void setEmbeddedReferenceBases(byte[] embeddedReferenceBases, int embeddedReferenceIndex, int zeroBasedStart)
      Set this CRAMReferenceRegion to use an embedded reference.
      Parameters:
      embeddedReferenceBases - the embedded reference bases to be used
      embeddedReferenceIndex - the reference ID used in the slice containing the embedded reference
      zeroBasedStart - the zero based reference start of the first base in the embedded reference bases

    • getFullContigLength

      public int getFullContigLength()
      Returns:
      the length of the entire reference contig maintained by this region. note that this is not the same as the length of the current bases maintained by this region (this can happen if the region contains a fragment, or an embedded reference fragment), or -1 if no current region is established