Package htsjdk.samtools.cram.ref

Class ReferenceContext

java.lang.Object
htsjdk.samtools.cram.ref.ReferenceContext
All Implemented Interfaces:
Comparable<ReferenceContext>
public class ReferenceContext extends Object implements Comparable<ReferenceContext>
ReferenceContext defines how a given Slice or Container relates to a reference sequence. There are 3 types of reference context: single-reference context, which is backed by an accompanying reference sequence ID, UNMAPPED_UNPLACED_ID/ReferenceContextType.UNMAPPED_UNPLACED_TYPE which indicates an unmapped/unplaced context, and MULTIPLE_REFERENCE_ID/ReferenceContextType.MULTIPLE_REFERENCE_TYPE) which indicates a multiple reference context.

  • Field Details

    • UNMAPPED_UNPLACED_ID

      public static final int UNMAPPED_UNPLACED_ID
      See Also:

    • MULTIPLE_REFERENCE_ID

      public static final int MULTIPLE_REFERENCE_ID
      See Also:

    • UNINITIALIZED_REFERENCE_ID

      public static final int UNINITIALIZED_REFERENCE_ID
      See Also:

    • MULTIPLE_REFERENCE_CONTEXT

      public static final ReferenceContext MULTIPLE_REFERENCE_CONTEXT

    • UNMAPPED_UNPLACED_CONTEXT

      public static final ReferenceContext UNMAPPED_UNPLACED_CONTEXT

  • Constructor Details

    • 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 Details

    • getType

      public ReferenceContextType getType()
      Get the ReferenceContext type: SINGLE_REFERENCE_TYPE, UNMAPPED_UNPLACED_TYPE, or MULTIPLE_REFERENCE_TYPE
      Returns:
      the ReferenceContextType enum

    • 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 reference 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

    • equals

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

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • compareTo

      public int compareTo(ReferenceContext o)
      Specified by:
      compareTo in interface Comparable<ReferenceContext>

    • toString

      public String toString()
      Overrides:
      toString in class Object