ADAM_2.12: Core 0.35.0 API < Back
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# Packages

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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
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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: 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]
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     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
7.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
8.  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

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

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

11.  def getStartBin(region: ReferenceRegion): Int

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

12.  def invert(bin: Int): ReferenceRegion

    Given a bin number, return its corresponding ReferenceRegion.

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

    The total number of bins induced by this partition.

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

### Deprecated Value Members

1.  def finalize(): Unit
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     protected[lang]
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     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from Product

### Inherited from Equals

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped