Package htsjdk.samtools

Class LinearIndex

java.lang.Object
htsjdk.samtools.LinearIndex
public class LinearIndex extends Object
The linear index associated with a given reference in a BAM index.

  • Field Details

    • MAX_LINEAR_INDEX_SIZE

      public static final int MAX_LINEAR_INDEX_SIZE

    • BAM_LIDX_SHIFT

      public static final int BAM_LIDX_SHIFT
      See Also:

  • Constructor Details

    • LinearIndex

      public LinearIndex(int referenceSequence, int indexStart, long[] indexEntries)

  • Method Details

    • getReferenceSequence

      public int getReferenceSequence()

    • size

      public int size()

    • get

      public long get(int index)

    • convertToLinearIndexOffset

      public static int convertToLinearIndexOffset(int contigPos)

    • getMinimumOffset

      public long getMinimumOffset(int startPos)
      Gets the minimum offset of any alignment start appearing in this index, according to the linear index.
      Parameters:
      startPos - Starting position for this query.
      Returns:
      The minimum offset, in chunk format, of any read appearing in this position.

    • getIndexEntries

      public long[] getIndexEntries()
      Direct access to the array. Be careful!
      Returns:
      The elements of the linear index.

    • getIndexStart

      public int getIndexStart()

    • equals

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

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object