Class ReferenceContext

    • Field Detail

      • UNINITIALIZED_REFERENCE_ID

        public static final int UNINITIALIZED_REFERENCE_ID
        See Also:
        Constant Field Values
      • MULTIPLE_REFERENCE_CONTEXT

        public static final ReferenceContext MULTIPLE_REFERENCE_CONTEXT
      • UNMAPPED_UNPLACED_CONTEXT

        public static final ReferenceContext UNMAPPED_UNPLACED_CONTEXT
    • Constructor Detail

      • ReferenceContext

        public ReferenceContext​(int referenceContextID)
        Create a ReferenceContext from a value that is either a valid sequence ID, or a reference context sentinel value: 0 or greater for single reference -1 for unmapped-unplaced -2 for multiple reference
        Parameters:
        referenceContextID - the sequence ID or sentinel value for constructing this ReferenceContext
    • Method Detail

      • getReferenceContextID

        public int getReferenceContextID()
        Get the ReferenceContext sequence ID, or, for unmapped or multiple context, a sentinel value suitable for serialization: 0 or greater for single reference -1 for unmapped -2 for multiple reference
        Returns:
        the sequence ID
      • getReferenceSequenceID

        public int getReferenceSequenceID()
        Get the valid reference sequence ID. May only be called if this is reference context of type single-reference (other reference context types don't have a valid sequence ID), otherwise see getReferenceContextID().
        Returns:
        the sequence ID for this refernce context
        Throws:
        CRAMException - if this is not a single-ref reference context
      • isUnmappedUnplaced

        public boolean isUnmappedUnplaced()
        Determine if this ReferenceContext represents unmapped-unplaced ?
        Returns:
        true if the ReferenceContext is ReferenceContextTypeUNMAPPED_UNPLACED_TYPE.
      • isMultiRef

        public boolean isMultiRef()
        Determine if this ReferenceContext represents: - reads placed on multiple references - or a combination of placed and unplaced reads?
        Returns:
        true if the ReferenceContext is
      • isMappedSingleRef

        public boolean isMappedSingleRef()
        Determine if this ReferenceContext represents a single reference.
        Returns:
        true if this ReferenceContext represents
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object