c

org.bdgenomics.adam.ds

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

Linear Supertypes
Product, Equals, Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. GenomeBins
  2. Product
  3. Equals
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

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: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. val binSize: Long
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. 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

  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. def getEndBin(region: ReferenceRegion): Int

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

  12. def getStartBin(region: ReferenceRegion): Int

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

  13. def invert(bin: Int): ReferenceRegion

    Given a bin number, return its corresponding ReferenceRegion.

  14. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  15. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  17. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  18. def numBins: Int

    The total number of bins induced by this partition.

  19. val seqLengths: Map[String, Long]
  20. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  21. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from Product

Inherited from Equals

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped