Class

org.bdgenomics.adam.rdd

GenomeBins

Related Doc: package rdd

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case class GenomeBins(binSize: Long, seqLengths: Map[String, Long]) extends Serializable with Product

Partition a genome into a set of bins.

Note that this class will not tolerate invalid input, so filter in advance if you use it.

binSize

The size of each bin in nucleotides

seqLengths

A map containing the length of each contig

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Product, Equals, Serializable, Serializable, AnyRef, Any
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  1. GenomeBins
  2. Product
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Instance Constructors

  1. new GenomeBins(binSize: Long, seqLengths: Map[String, Long])

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    binSize

    The size of each bin in nucleotides

    seqLengths

    A map containing the length of each contig

Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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

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  4. final def asInstanceOf[T0]: T0

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  5. val binSize: Long

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    The size of each bin in nucleotides

  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
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    @throws( ... )
  7. final def eq(arg0: AnyRef): Boolean

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  8. def finalize(): Unit

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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )
  9. def get(region: ReferenceRegion, useStart: Boolean = true): Int

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    Get the bin number corresponding to a query ReferenceRegion.

    Get the bin number corresponding to a query ReferenceRegion.

    region

    the query ReferenceRegion

    useStart

    whether to use the start or end point of region to pick the bin

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

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    Definition Classes
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  11. def getEndBin(region: ReferenceRegion): Int

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    Get the bin number corresponding to the end of the query ReferenceRegion.

  12. def getStartBin(region: ReferenceRegion): Int

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    Get the bin number corresponding to the start of the query ReferenceRegion.

  13. def invert(bin: Int): ReferenceRegion

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    Given a bin number, return its corresponding ReferenceRegion.

  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. def numBins: Int

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    The total number of bins induced by this partition.

  19. val seqLengths: Map[String, Long]

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    A map containing the length of each contig

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

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  21. final def wait(): Unit

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    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit

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

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Inherited from Product

Inherited from Equals

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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