org.hammerlab.guacamole.loci.partitioning

CappedRegionsPartitioner

class CappedRegionsPartitioner[R <: ReferenceRegion] extends LociPartitioner

Loci-partitioner that guarantees at most @maxRegionsPerPartition regions per partition.

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LociPartitioner, AnyRef, Any
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Instance Constructors

  1. new CappedRegionsPartitioner(regions: RDD[R], halfWindowSize: Int, maxRegionsPerPartition: Int, printPartitioningStats: Boolean, explodeCoverage: Boolean, trimRanges: Boolean)(implicit arg0: ClassTag[R])

    regions

    regions to partition loci based on.

    halfWindowSize

    consider regions to overlap loci that their ends are within this many base-pairs of.

    maxRegionsPerPartition

    cap partitions at this many regions.

    printPartitioningStats

    print some statistics about the computed partitioning; adds several Spark stages so should be skipped for performance-critical runs.

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 finalize(): Unit

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

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  12. def hashCode(): Int

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  13. final def isInstanceOf[T0]: Boolean

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

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  15. final def notify(): Unit

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  16. final def notifyAll(): Unit

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  17. def partition(loci: LociSet): LociPartitioning

    Definition Classes
    CappedRegionsPartitioner → LociPartitioner

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

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  19. def toString(): String

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  20. final def wait(): Unit

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

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

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Inherited from LociPartitioner

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