Package htsjdk.samtools.cram.structure

Class SliceBlocks

  • public class SliceBlocks
extends Object
    Manage the (logical) set of blocks that constitute a Slice, not including the Slice header block, which is managed by Slice. Prevents duplicate blocks (blocks with non-unique content ID) or illogical blocks (i.e., setting a core block that is not of type core block, or an external block that is not an external block) from being added.

    • Constructor Detail

      • SliceBlocks

        public SliceBlocks​(Block coreBlock,
                   List<Block> externalBlocks)
        Create a new SliceBlocks object from a core block and one or more external blocks.
        Parameters:
        coreBlock - the core block for the Slice, may not be null
        externalBlocks - the external blocks for this Slice, may not be null and must contain a least one block

      • SliceBlocks

        public SliceBlocks​(CRAMVersion cramVersion,
                   int numberOfBlocks,
                   InputStream inputStream)
        Read the set of blocks that make up a slice from a CRAM stream.
        Parameters:
        cramVersion - CRAM version being read
        numberOfBlocks - number of blocks to consume from the stream
        inputStream - stream to consume

    • Method Detail

      • getCoreBlock

        public Block getCoreBlock()
        Return the core block for this Slice. May be null.

      • getExternalBlock

        public Block getExternalBlock​(Integer contentID)
        Get the external block corresponding to a contentID.
        Parameters:
        contentID - contentID identifying the external block
        Returns:
        external block for the contentID. May be null.

      • getExternalContentIDs

        public List<Integer> getExternalContentIDs()
        Return a list of external content IDs. May be empty. For each content ID returned, the corresponding external block can be obtained using getExternalBlock(java.lang.Integer).
        Returns:
        list of external content IDs

      • getNumberOfExternalBlocks

        public int getNumberOfExternalBlocks()
        Number of external locks present in this SliceBlocks object (does not include the core block).
        Returns:
        number of external blocks, including any embedded reference block, but excluding the core block

      • writeBlocks

        public void writeBlocks​(CRAMVersion cramVersion,
                        OutputStream outputStream)
        Write the coreBlock and each external block out to a CRAM stream. There is no predefined order that must be honored, since each block is identified by a unique contentID.
        Parameters:
        cramVersion - CRAM major version being written
        outputStream - stream to write blocks to