ADAM_2.12: Core 0.33.0 API < Back
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# 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

# GenomicRegionPartitioner 

###
Companion object GenomicRegionPartitioner

#### case class GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true) extends Partitioner with Logging with Product with Serializable

A partitioner for ReferenceRegion-keyed data.

partitionSize

  The number of bases per partition.

seqLengths

  A map between contig names and contig lengths.

start

  If true, use the start position (instead of the end position) to decide which partition a key belongs to.

Linear Supertypes
Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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Ordering

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2. By Inheritance

Inherited

1. GenomicRegionPartitioner
2. Product
3. Equals
4. Logging
5. Partitioner
6. Serializable
7. Serializable
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true)

   partitionSize

     The number of bases per partition.

   seqLengths

     A map between contig names and contig lengths.

   start

     If true, use the start position (instead of the end position) to decide which partition a key belongs to.

### 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.  def clone(): AnyRef
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
6.  def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
7.  def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
8.  def debug(msg: ⇒ Any): Unit
   Attributes
     protected
   Definition Classes
     Logging
9.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
11.  def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
12.  def error(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
13.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
14.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
15.  def getPartition(key: Any): Int

    key

      The key to get the partition index for.

    returns

      The partition that a key should map to.

    Definition Classes
      GenomicRegionPartitioner → Partitioner
    Exceptions thrown

      `IllegalArgumentException` Throws an exception if the data is not a ReferenceRegion or a tuple of (ReferenceRegion, _).

16.  def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
17.  def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
18.  def info(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
19.  def isDebugEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
20.  def isErrorEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
21.  def isInfoEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
22.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
23.  def isTraceEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
24.  def isWarnEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
25.  def logger: Logger
    Attributes
      protected
    Definition Classes
      Logging
26.  def loggerName: String
    Attributes
      protected
    Definition Classes
      Logging
27.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
28.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
29.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
30.  def numPartitions: Int

    returns

      The number of partitions described by this partitioner. Roughly the size of the genome divided by the partition length.

    Definition Classes
      GenomicRegionPartitioner → Partitioner
31.  val partitionSize: Long
32.  val seqLengths: Map[String, Long]
33.  val start: Boolean
34.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
35.  def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
36.  def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
37.  def trace(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
38.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
39.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
40.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
41.  def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
42.  def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
43.  def warn(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging

### Inherited from Product

### Inherited from Equals

### Inherited from Logging

### Inherited from Partitioner

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped