SequenceDictionary

Value Members

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

   

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2. final def ##(): Int

   

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3. def +(record: SequenceRecord): SequenceDictionary

   

4. def ++(that: SequenceDictionary): SequenceDictionary

   

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

   

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6. def apply(name: String): Option[SequenceRecord]

   

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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9. def containsRefName(name: String): Boolean

   

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

    

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11. def equals(o: Any): Boolean

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

12. def finalize(): Unit

    

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    protected[java.lang]

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

13. final def getClass(): Class[_]

    

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14. def hashCode(): Int

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

15. def isCompatibleWith(that: SequenceDictionary): Boolean

    

16. def isEmpty: Boolean

    

17. final def isInstanceOf[T0]: Boolean

    

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18. final def ne(arg0: AnyRef): Boolean

    

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19. final def notify(): Unit

    

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20. final def notifyAll(): Unit

    

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21. val records: Vector[SequenceRecord]

    

22. def sorted: SequenceDictionary

    

    Sort the records in a sequence dictionary.

    Sort the records in a sequence dictionary.

    returns

    Returns a new sequence dictionary where the sequence records are sorted. If the sequence records have indices, the records will be sorted by their indices. If not, the sequence records will be sorted lexically by contig name.

    See also

    stripIndices

23. def stripIndices: SequenceDictionary

    

    Strips indices from a Sequence Dictionary.

    Strips indices from a Sequence Dictionary.

    returns

    This returns a new sequence dictionary devoid of indices. This is important for sorting: the default sort in ADAM is based on a lexical ordering, while the default sort in SAM is based on sequence indices. If the indices are not stripped before a file is saved back to SAM/BAM, the SAM/BAM header sequence ordering will not match the sort order of the records in the file.

    See also

    sorted

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

    

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25. def toSAMSequenceDictionary: SAMSequenceDictionary

    

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    returns

    Returns a SAM formatted sequence dictionary.

26. def toString(): String

    

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    SequenceDictionary → AnyRef → Any

27. final def wait(): Unit

    

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

    

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

    

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