SequenceDictionary

Value Members

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

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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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

   

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   protected[java.lang]

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   @throws( ... )

9. def empty: SequenceDictionary

   
   returns

   Creates a new, empty SequenceDictionary.

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

    

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11. def equals(arg0: Any): Boolean

    

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12. def finalize(): Unit

    

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    protected[java.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.

    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

    fromVCFHeader

    fromSAMHeader

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

    

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

    

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