org.bdgenomics.adam.rdd

MultiContigNonoverlappingRegions

class MultiContigNonoverlappingRegions extends Serializable

Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.

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Instance Constructors

  1. new MultiContigNonoverlappingRegions(seqDict: SequenceDictionary, regions: Seq[(Int, Seq[ReferenceRegion])])

    seqDict

    A sequence dictionary for all the possible reference regions that could be aligned to.

    regions

    A Seq of ReferencRegions, pre-partitioned by their refIds -- so, for a given pair (x, regs) in this Seq, all regions R in regs must satisfy R.refId == x. Furthermore, all the x's must be valid refIds with respect to the sequence dictionary.

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. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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

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  9. def equals(arg0: Any): Boolean

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  10. def filter[U](value: U)(implicit mapping: ReferenceMapping[U]): Boolean

  11. def finalize(): Unit

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

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  13. def hashCode(): Int

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  14. final def isInstanceOf[T0]: Boolean

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

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  16. final def notify(): Unit

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  17. final def notifyAll(): Unit

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  18. val regionMap: Map[Int, NonoverlappingRegions]

  19. def regionsFor[U](regionable: U)(implicit mapping: ReferenceMapping[U]): Iterable[ReferenceRegion]

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

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  21. def toString(): String

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  22. final def wait(): Unit

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

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

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