SequenceDictionary

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

    Attributes

    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

    Attributes

    protected[java.lang]

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    Annotations

    @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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21. final def ne(arg0: AnyRef): 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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    @throws( ... )

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

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

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