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. def +(record: SequenceRecord): SequenceDictionary

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

6. final def ==(arg0: AnyRef): Boolean

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

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

9. final def asInstanceOf[T0]: T0

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10. def clone(): AnyRef

    Attributes

    protected[java.lang]

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11. def containsRefName(name: String): Boolean

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

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13. def equals(o: Any): Boolean

    Definition Classes

    SequenceDictionary → AnyRef → Any

14. def finalize(): Unit

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    protected[java.lang]

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

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

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16. def hashCode(): Int

    Definition Classes

    SequenceDictionary → AnyRef → Any

17. def isCompatibleWith(that: SequenceDictionary): Boolean

18. def isEmpty: Boolean

19. final def isInstanceOf[T0]: Boolean

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

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21. final def notify(): Unit

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22. final def notifyAll(): Unit

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23. val records: Vector[SequenceRecord]

24. 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

25. 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

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

    Definition Classes

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27. 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.

28. def toString(): String

    Definition Classes

    SequenceDictionary → AnyRef → Any

29. final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

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

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    @throws( ... )