Package htsjdk.samtools.cram.structure

Class ContainerHeader

java.lang.Object
htsjdk.samtools.cram.structure.ContainerHeader
public class ContainerHeader extends Object

  • Constructor Details

    • ContainerHeader

      public ContainerHeader(AlignmentContext alignmentContext, int blockCount, int containerBlocksByteSize, int recordCount, long globalRecordCounter, long baseCount, List<Integer> landmarks, int checksum)
      Create a ContainerHeader.
      Parameters:
      alignmentContext - the alignment context for this container
      blockCount - block count for this container
      containerBlocksByteSize -
      recordCount - record count for this container
      globalRecordCounter - global record count for this container
      baseCount - base count for this container
      landmarks - List of landmarks for this container (may be empty)
      checksum -

    • ContainerHeader

      public ContainerHeader(AlignmentContext alignmentContext, int blockCount, int recordCount, long globalRecordCounter, int baseCount)
      Create a Container from a partial set of values. Used in cases where we don't yet have all of the values (such as landmarks, which, being stream offsets, can't be calculated until the container is written out to a stream).
      Parameters:
      alignmentContext - the alignment context for this container
      blockCount - block count for this container
      recordCount - record count for this container
      globalRecordCounter - global record count for this container
      baseCount - base count for this container

    • ContainerHeader

      public ContainerHeader(CRAMVersion cramVersion, InputStream inputStream)
      Create a container header from an InputStream.
      Parameters:
      cramVersion - the CRAM version to assume
      inputStream - the input stream from which to read

  • Method Details

    • makeSAMFileHeaderContainer

      public static ContainerHeader makeSAMFileHeaderContainer(int containerBlocksByteSize)
      Create a ContainerHeader for a SAMFileHeader container.
      Parameters:
      containerBlocksByteSize - size of the SAMFileHeader block to be embedded in this container

    • getContainerBlocksByteSize

      public int getContainerBlocksByteSize()

    • setContainerBlocksByteSize

      public void setContainerBlocksByteSize(int containerBlocksByteSize)

    • getAlignmentContext

      public AlignmentContext getAlignmentContext()

    • getNumberOfRecords

      public int getNumberOfRecords()

    • getGlobalRecordCounter

      public long getGlobalRecordCounter()

    • getBaseCount

      public long getBaseCount()

    • getBlockCount

      public int getBlockCount()

    • getLandmarks

      public List<Integer> getLandmarks()

    • setLandmarks

      public void setLandmarks(List<Integer> landmarks)

    • getChecksum

      public int getChecksum()

    • write

      public int write(CRAMVersion cramVersion, OutputStream outputStream)
      Write CRAM Container (header only) out into the given OutputStream.
      Parameters:
      cramVersion - CRAM version
      outputStream - the output stream to write the container header to
      Returns:
      number of bytes written out to the output stream

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • isEOF

      public boolean isEOF()