Package htsjdk.samtools

Class Chunk

java.lang.Object
htsjdk.samtools.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:

  • Constructor Details

    • Chunk

      public Chunk(long start, long end)

  • Method Details

    • clone

      public Chunk clone()
      Overrides:
      clone in class Object

    • getChunkStart

      public long getChunkStart()

    • setChunkStart

      protected void setChunkStart(long value)

    • getChunkEnd

      public long getChunkEnd()

    • setChunkEnd

      protected void setChunkEnd(long value)

    • compareTo

      public int compareTo(Chunk chunk)
      Specified by:
      compareTo in interface Comparable<Chunk>

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • 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

    • toString

      public String toString()
      Overrides:
      toString 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.