org.bdgenomics.adam.rdd

GenomeBins

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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Instance Constructors

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

    binSize

    The size of each bin in nucleotides

    seqLengths

    A map containing the length of each contig

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

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

    Definition Classes
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  6. final def asInstanceOf[T0]: T0

    Definition Classes
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  7. val binSize: Long

    The size of each bin in nucleotides

  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
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    Annotations
    @throws( ... )

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

    Definition Classes
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  10. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
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    @throws( classOf[java.lang.Throwable] )

  11. def get(region: ReferenceRegion, useStart: Boolean = true): Int

    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

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

    Definition Classes
    AnyRef → Any

  13. def getEndBin(region: ReferenceRegion): Int

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

  14. def getStartBin(region: ReferenceRegion): Int

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

  15. def invert(bin: Int): ReferenceRegion

    Given a bin number, return its corresponding ReferenceRegion.

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
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  17. final def ne(arg0: AnyRef): Boolean

    Definition Classes
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  18. final def notify(): Unit

    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  20. def numBins: Int

    The total number of bins induced by this partition.

  21. val seqLengths: Map[String, Long]

    A map containing the length of each contig

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

    Definition Classes
    AnyRef

  23. final def wait(): Unit

    Definition Classes
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

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Inherited from Product

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