Package org.broadinstitute.hellbender.utils.reference

Class ReferenceBases

java.lang.Object
org.broadinstitute.hellbender.utils.reference.ReferenceBases
All Implemented Interfaces:
Serializable
public final class ReferenceBases extends Object implements Serializable
ReferenceBases stores the bases of the reference genome for a particular interval. This class requires the bases to be encoded at 8 bits per base.
See Also:

  • Constructor Details

    • ReferenceBases

      public ReferenceBases(byte[] bases, SimpleInterval interval)

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • equals

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

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • getBases

      public byte[] getBases()

    • getInterval

      public SimpleInterval getInterval()

    • getSubset

      public ReferenceBases getSubset(SimpleInterval subsetInterval)
      getSubset returns only the bases of the interval passed in.
      Parameters:
      subsetInterval - , the subset to be returned
      Returns:
      the subset of ReferenceBases