Package htsjdk.samtools

Class CRAMContainerStreamWriter

java.lang.Object
htsjdk.samtools.CRAMContainerStreamWriter
public class CRAMContainerStreamWriter extends Object
Class for writing SAMRecords into a series of CRAM containers on an output stream, with an optional index.

  • Constructor Details

    • CRAMContainerStreamWriter

      public CRAMContainerStreamWriter(OutputStream recordOutputStream, OutputStream indexOutputStream, CRAMReferenceSource source, SAMFileHeader samFileHeader, String outputIdentifier)
      Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
      Parameters:
      recordOutputStream - where to write the CRAM stream.
      indexOutputStream - where to write the output index. Can be null if no index is required.
      source - reference cramReferenceSource
      samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.
      outputIdentifier - used for display in error message display

    • CRAMContainerStreamWriter

      public CRAMContainerStreamWriter(OutputStream outputStream, CRAMReferenceSource source, SAMFileHeader samFileHeader, String outputIdentifier, CRAMIndexer indexer)
      Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
      Parameters:
      outputStream - where to write the CRAM stream.
      source - reference cramReferenceSource
      samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.
      outputIdentifier - used for display in error message display
      indexer - CRAM indexer. Can be null if no index is required.

    • CRAMContainerStreamWriter

      public CRAMContainerStreamWriter(CRAMEncodingStrategy encodingStrategy, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, OutputStream outputStream, CRAMIndexer indexer, String outputIdentifier)
      Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
      Parameters:
      encodingStrategy - encoding strategy values
      referenceSource - reference cramReferenceSource
      samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.
      outputStream - where to write the CRAM stream.
      indexer - CRAM indexer. Can be null if no index is required.
      outputIdentifier - informational string included in error reporting

  • Method Details

    • writeAlignment

      public void writeAlignment(SAMRecord alignment)
      Accumulate alignment records until we meet the threshold to flush a container.
      Parameters:
      alignment - must not be null

    • writeHeader

      public void writeHeader(SAMFileHeader requestedSAMFileHeader)
      Write a CRAM file header and the previously provided SAM header to the stream.

    • writeHeader

      public void writeHeader()
      Write a CRAM file header and the previously provided SAM header to the stream.

    • finish

      public void finish(boolean writeEOFContainer)
      Finish writing to the stream. Flushes the record cache and optionally emits an EOF container.
      Parameters:
      writeEOFContainer - true if an EOF container should be written. Only use false if writing a CRAM file fragment which will later be aggregated into a complete CRAM file.

    • writeContainer

      protected void writeContainer(Container container)