org.bdgenomics.adam.rdd

# GenomicPositionPartitioner

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Related Docs: object GenomicPositionPartitioner | package rdd

#### case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long]) extends Partitioner with Logging with Product with Serializable

GenomicPositionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.

This can be used to organize genomic data for computation that is spatially distributed (e.g. GATK and Queue's "scatter-and-gather" for locus-parallelizable walkers).

numParts

  The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.

seqLengths

  a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.

Linear Supertypes
Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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1. GenomicPositionPartitioner
2. Product
3. Equals
4. Logging
5. Partitioner
6. Serializable
7. Serializable
8. AnyRef
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### Instance Constructors

1. #### new GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long])

   numParts

     The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.

   seqLengths

     a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.

### Value Members

1. #### final def !=(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

2. #### final def ##(): Int

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     AnyRef → Any

3. #### final def ==(arg0: Any): Boolean

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     AnyRef → Any

4. #### final def asInstanceOf[T0]: T0

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5. #### def clone(): AnyRef

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     protected[java.lang]
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     @throws( ... )

6. #### def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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     protected
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     Logging

7. #### def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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8. #### def debug(msg: ⇒ Any): Unit

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

   Definition Classes
     AnyRef

10. #### def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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      Logging

11. #### def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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12. #### def error(msg: ⇒ Any): Unit

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13. #### def finalize(): Unit

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

14. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

15. #### def getPartition(key: Any): Int

    Computes the partition for a key.

    Computes the partition for a key.

    key

      A key to compute the partition for.

    returns

      The partition that this key belongs to.

    Definition Classes
      GenomicPositionPartitioner → Partitioner
    Exceptions thrown

      `IllegalArgumentException` if the key is not a ReferencePosition, or (ReferencePosition, _) tuple.

16. #### def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
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      Logging

17. #### def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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18. #### def info(msg: ⇒ Any): Unit

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19. #### def isDebugEnabled: Boolean

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20. #### def isErrorEnabled: Boolean

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21. #### def isInfoEnabled: Boolean

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22. #### final def isInstanceOf[T0]: Boolean

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23. #### def isTraceEnabled: Boolean

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24. #### def isWarnEnabled: Boolean

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25. #### def logger: Logger

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      Logging

26. #### def loggerName: String

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      Logging

27. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

28. #### final def notify(): Unit

    Definition Classes
      AnyRef

29. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

30. #### def numPartitions: Int

    This is the total number of partitions for both mapped and unmapped positions.

    This is the total number of partitions for both mapped and unmapped positions. All unmapped positions go into the last partition.

    Definition Classes
      GenomicPositionPartitioner → Partitioner
    See also

      parts

31. #### val numParts: Int

    The number of equally-sized regions into which the total genomic space is partitioned; the total number of partitions is numParts + 1, with the "+1" resulting from one extra partition that is used to capture null or UNMAPPED values of the ReferencePosition type.

32. #### val seqLengths: Map[String, Long]

    a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.

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

    Definition Classes
      AnyRef

34. #### def toString(): String

    Definition Classes
      GenomicPositionPartitioner → AnyRef → Any

35. #### def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

    Attributes
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      Logging

36. #### def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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37. #### def trace(msg: ⇒ Any): Unit

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38. #### final def wait(): Unit

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      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
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      @throws( ... )

40. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
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      @throws( ... )

41. #### def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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      Logging

42. #### def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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43. #### def warn(msg: ⇒ Any): Unit

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### Inherited from Product

### Inherited from Equals

### Inherited from Logging

### Inherited from Partitioner

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped