org.bdgenomics.adam.models

# SequenceDictionary

#### object SequenceDictionary extends Serializable

SequenceDictionary contains the (bijective) map between Ints (the referenceId) and Strings (the referenceName) from the header of a BAM file, or the combined result of multiple such SequenceDictionaries.

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### 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
     AnyRef

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

   Definition Classes
     Any

6. #### def apply(reader: SamReader): SequenceDictionary

7. #### def apply(header: SAMFileHeader): SequenceDictionary

8. #### def apply(dict: SAMSequenceDictionary): SequenceDictionary

9. #### def apply(records: SequenceRecord*): SequenceDictionary

10. #### final def asInstanceOf[T0]: T0

    Definition Classes
      Any

11. #### def clone(): AnyRef

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

12. #### def empty: SequenceDictionary

    returns

      Creates a new, empty SequenceDictionary.

13. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

14. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

15. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

16. #### def fromAvro(contigs: Seq[Contig]): SequenceDictionary

    Creates a sequence dictionary from a sequence of Avro Contigs.

    Creates a sequence dictionary from a sequence of Avro Contigs.

    contigs

      Seq of Contig records.

    returns

      Returns a sequence dictionary.

17. #### def fromSAMHeader(header: SAMFileHeader): SequenceDictionary

    Extracts a SAM sequence dictionary from a SAM file header and returns an ADAM sequence dictionary.

    Extracts a SAM sequence dictionary from a SAM file header and returns an ADAM sequence dictionary.

    header

      SAM file header.

    returns

      Returns an ADAM style sequence dictionary.

    See also

      fromSAMSequenceDictionary

18. #### def fromSAMReader(samReader: SamReader): SequenceDictionary

19. #### def fromSAMSequenceDictionary(samDict: SAMSequenceDictionary): SequenceDictionary

    Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.

    Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.

    samDict

      SAM style sequence dictionary.

    returns

      Returns an ADAM style sequence dictionary.

    See also

      fromVCFHeader

      fromSAMHeader

20. #### def fromVCFHeader(header: VCFHeader): SequenceDictionary

    Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.

    Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.

    header

      VCF file header.

    returns

      Returns an ADAM style sequence dictionary.

    See also

      fromSAMHeader

21. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

22. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

23. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
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24. #### final def ne(arg0: AnyRef): Boolean

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25. #### final def notify(): Unit

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26. #### final def notifyAll(): Unit

    Definition Classes
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27. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

28. #### def toSAMSequenceDictionary(dictionary: SequenceDictionary): SAMSequenceDictionary

29. #### def toString(): String

    Definition Classes
      AnyRef → Any

30. #### final def wait(): Unit

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      AnyRef
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      @throws( ... )

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

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      @throws( ... )

32. #### final def wait(arg0: Long): Unit

    Definition Classes
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      @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

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