ADAM_2.12: Core 0.32.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package rdd
  Definition Classes
    adam
-  package feature
  Definition Classes
    rdd
-  package fragment
  Definition Classes
    rdd
-  package read
  Definition Classes
    rdd
-  package sequence
  Definition Classes
    rdd
-  package variant
  Definition Classes
    rdd
- ADAMContext
- ADAMSaveAnyArgs
- AvroGenomicDataset
- AvroReadGroupGenomicDataset
- DatasetBoundGenericGenomicDataset
- DatasetBoundGenomicDataset
- FullOuterShuffleRegionJoin
- GenericConverter
- GenericGenomicDataset
- GenomeBins
- GenomicBroadcast
- GenomicDataset
- GenomicDatasetConversion
- GenomicDatasetWithLineage
- GenomicPositionPartitioner
- GenomicRegionPartitioner
- InFormatter
- InFormatterCompanion
- InnerShuffleRegionJoin
- InnerShuffleRegionJoinAndGroupByLeft
- InnerTreeRegionJoin
- InnerTreeRegionJoinAndGroupByRight
- LeftOuterShuffleRegionJoin
- LeftOuterShuffleRegionJoinAndGroupByLeft
- MultisampleAvroGenomicDataset
- MultisampleGenomicDataset
- OutFormatter
- RDDBoundGenericGenomicDataset
- ReferencePartitioner
- RegionJoin
- RightOuterShuffleRegionJoinAndGroupByLeft
- RightOuterTreeRegionJoin
- RightOuterTreeRegionJoinAndGroupByRight
- ShuffleRegionJoin
- SortedIntervalPartitionJoinWithVictims
- TreeRegionJoin
- VictimlessSortedIntervalPartitionJoin

c

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

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[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
7.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
8.  def finalize(): Unit
   Attributes
     protected[java.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
      @native() @throws( ... )

### Inherited from Product

### Inherited from Equals

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped