org.bdgenomics.adam.rdd

# 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.

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Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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1. GenomicRegionPartitioner
2. Product
3. Equals
4. Logging
5. Partitioner
6. Serializable
7. Serializable
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### 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: AnyRef): Boolean

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

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

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4. #### final def ==(arg0: AnyRef): Boolean

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

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

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

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     @throws( ... )

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

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

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

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

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11. #### 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, _).

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

    Definition Classes
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13. #### def isTraceEnabled(): Boolean

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      protected
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      Logging

14. #### def log: Logger

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      Logging

15. #### def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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      protected
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      Logging

16. #### def logDebug(msg: ⇒ String): Unit

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17. #### def logError(msg: ⇒ String, throwable: Throwable): Unit

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      protected
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      Logging

18. #### def logError(msg: ⇒ String): Unit

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19. #### def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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      protected
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20. #### def logInfo(msg: ⇒ String): Unit

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21. #### def logName: String

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22. #### def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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23. #### def logTrace(msg: ⇒ String): Unit

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24. #### def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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25. #### def logWarning(msg: ⇒ String): Unit

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

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

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

    Definition Classes
      AnyRef

29. #### 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

30. #### val partitionSize: Long

    The number of bases per partition.

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

    A map between contig names and contig lengths.

32. #### val start: Boolean

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

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

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

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      @throws( ... )

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

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36. #### final def wait(arg0: Long): 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