Class/Object

org.bdgenomics.adam.rdd

GenomicRegionPartitioner

Related Docs: object GenomicRegionPartitioner | package rdd

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

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

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    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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  6. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  7. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  8. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  9. def getPartition(key: Any): Int

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    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, _).

  10. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  11. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  12. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  14. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  16. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  18. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  19. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  21. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  23. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  24. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  25. final def notify(): Unit

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    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  27. def numPartitions: Int

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    returns

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

    Definition Classes
    GenomicRegionPartitioner → Partitioner

  28. val partitionSize: Long

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    The number of bases per partition.

  29. val seqLengths: Map[String, Long]

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    A map between contig names and contig lengths.

  30. val start: Boolean

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

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

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    Definition Classes
    AnyRef

  32. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  34. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from Partitioner

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped