object SequenceDictionary extends Serializable

Singleton object for creating SequenceDictionaries.

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  1. final def !=(arg0: Any): Boolean
    Definition Classes
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  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. 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.

  5. 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.

  6. 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.

  7. final def asInstanceOf[T0]: T0
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  8. def clone(): AnyRef
    Attributes
    protected[lang]
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    @throws( ... ) @native()
  9. def empty: SequenceDictionary

    returns

    Creates a new, empty SequenceDictionary.

  10. final def eq(arg0: AnyRef): Boolean
    Definition Classes
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  11. def equals(arg0: Any): Boolean
    Definition Classes
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  12. def finalize(): Unit
    Attributes
    protected[lang]
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    @throws( classOf[java.lang.Throwable] )
  13. def fromAvro(references: Seq[Reference]): SequenceDictionary

    Creates a sequence dictionary from a sequence of Avro References.

    Creates a sequence dictionary from a sequence of Avro References.

    references

    Seq of Reference records.

    returns

    Returns a sequence dictionary.

  14. 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

    fromSAMHeader

    fromVCFHeader

  15. 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

  16. final def getClass(): Class[_]
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    @native()
  17. def hashCode(): Int
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  18. final def isInstanceOf[T0]: Boolean
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  19. final def ne(arg0: AnyRef): Boolean
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  20. final def notify(): Unit
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  21. final def notifyAll(): Unit
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  22. final def synchronized[T0](arg0: ⇒ T0): T0
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  23. def toString(): String
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  24. final def wait(): Unit
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    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  26. final def wait(arg0: Long): Unit
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Inherited from Serializable

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