SequenceDictionary

Value Members

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

   Definition Classes

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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(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

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11. def clone(): AnyRef

    Attributes

    protected[java.lang]

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    @throws( ... )

12. def empty: SequenceDictionary

    returns

    Creates a new, empty SequenceDictionary.

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

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14. def equals(arg0: Any): Boolean

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15. def finalize(): Unit

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    protected[java.lang]

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    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

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22. def hashCode(): Int

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23. final def isInstanceOf[T0]: Boolean

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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

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

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28. def toSAMSequenceDictionary(dictionary: SequenceDictionary): SAMSequenceDictionary

29. def toString(): String

    Definition Classes

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30. final def wait(): Unit

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    @throws( ... )

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

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

    Definition Classes

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    @throws( ... )