Package htsjdk.samtools

Class Chunk

  • All Implemented Interfaces:
    Serializable, Cloneable, Comparable<Chunk>
    public class Chunk
extends Object
implements Cloneable, Serializable, Comparable<Chunk>
    A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. A chunk is represented as a single 64-bit value where the high-order 48 bits point to the location of the start of a compressed BGZF block within a BGZF file and the low-order 16 bits point to a position within the decompressed data in the BGZF block. See the SAM/BAM spec for more details.
    See Also:
    Serialized Form

    • Constructor Detail

      • Chunk

        public Chunk​(long start,
             long end)

    • Method Detail

      • getChunkStart

        public long getChunkStart()

      • setChunkStart

        protected void setChunkStart​(long value)

      • getChunkEnd

        public long getChunkEnd()

      • setChunkEnd

        protected void setChunkEnd​(long value)

      • overlaps

        public boolean overlaps​(Chunk other)
        Returns whether two chunks overlap.
        Parameters:
        other - Chunk to which this should be compared.
        Returns:
        True if the chunks overlap. Returns false if the two chunks abut or are disjoint.

      • isAdjacentTo

        public boolean isAdjacentTo​(Chunk other)
        Returns whether two chunks overlap.
        Parameters:
        other - Chunk to which this should be compared.
        Returns:
        True if the two chunks are adjacent. Returns false if the chunks overlap or are discontinuous.

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object

      • optimizeChunkList

        public static List<Chunk> optimizeChunkList​(List<Chunk> chunks,
                                            long minimumOffset)
        Parameters:
        minimumOffset - Discard chunks that end before this file offset.
        Returns:
        sorted list of chunks in which adjacent chunks are coalesced.