org.bdgenomics.adam.models

# SequenceDictionary

#### object SequenceDictionary extends Serializable

Singleton object for creating SequenceDictionaries.

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### Value Members

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

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

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3. #### final def ##(): Int

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

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

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

   Makes a SequenceDictionary from a SAMFileHeader.

   Makes a SequenceDictionary from a SAMFileHeader.

   header

     htsjdk SAMFileHeader to extract sequences from.

   returns

     A SequenceDictionary with populated sequence records.

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

   Builds a sequence dictionary from an htsjdk SAMSequenceDictionary.

   Builds a sequence dictionary from an htsjdk SAMSequenceDictionary.

   dict

     Htsjdk sequence dictionary to build from.

   returns

     A SequenceDictionary with populated sequence records.

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

   Builds a sequence dictionary for a variable length collection of records.

   Builds a sequence dictionary for a variable length collection of records.

   records

     Records to include in the dictionary.

   returns

     A sequence dictionary containing these records.

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

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

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      protected[java.lang]
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      @throws( ... )

11. #### def empty: SequenceDictionary

    returns

      Creates a new, empty SequenceDictionary.

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

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

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

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

15. #### 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.

16. #### 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

17. #### 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

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

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

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

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

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

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

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

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

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

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

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