ReferenceBroadcast

Value Members

1. final def !=(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

2. final def !=(arg0: Any): Boolean

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

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5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. val broadcastedContigs: Map[String, ContigSequence]

8. def buildMdTag(readSequence: String, referenceContig: String, referenceStart: Int, cigar: Cigar): String

   Build a new MDTag from the reference and read sequence

   Build a new MDTag from the reference and read sequence

   readSequence

   Bases from the read

   referenceContig

   Name of the reference contig or chromosome

   referenceStart

   Start position of the read on the reference

   cigar

   CIGAR for the read on the reference

   returns

   MdTag for the the read

   Definition Classes

   ReferenceGenome

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

10. final def eq(arg0: AnyRef): Boolean

    Definition Classes

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11. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

    @throws( classOf[java.lang.Throwable] )

12. final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

13. def getContig(contigName: String): ContigSequence

    Retrieve a full contig/chromosome sequence

    Retrieve a full contig/chromosome sequence

    contigName

    contig/chromosome to retrieve reference sequence from

    returns

    Full sequence associated with the contig

    Definition Classes

    ReferenceBroadcast → ReferenceGenome

14. def getReferenceBase(contigName: String, locus: Int): Byte

    Retrieve a reference base on a given contig at a given locus

    Retrieve a reference base on a given contig at a given locus

    contigName

    contig/chromosome to retrieve reference sequence from

    locus

    position in the sequence to retrieve

    returns

    Base at the given reference position

    Definition Classes

    ReferenceBroadcast → ReferenceGenome

15. def getReferenceSequence(contigName: String, startLocus: Int, endLocus: Int): Array[Byte]

    Get the reference base at the given reference location

    Get the reference base at the given reference location

    contigName

    contig/chromosome to retrieve reference sequence from

    startLocus

    0-based inclusive start of the subsequence

    endLocus

    0-based exclusive end of the subsequence

    returns

    Array of bases for the reference sequence

    Definition Classes

    ReferenceBroadcast → ReferenceGenome

16. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

17. final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

18. final def notify(): Unit

    Definition Classes

    AnyRef

19. final def notifyAll(): Unit

    Definition Classes

    AnyRef

20. val source: Option[String]

    Path where this reference was loaded from, or other description of its provenance (optional).

    Path where this reference was loaded from, or other description of its provenance (optional).

    For provenance tracking only. Not guaranteed to be a valid path or on a filesystem that is currently accessible.

    Definition Classes

    ReferenceBroadcast → ReferenceGenome

21. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

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22. final def wait(): Unit

    Definition Classes

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    Annotations

    @throws( ... )

23. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes

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    Annotations

    @throws( ... )

24. final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )