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.

Linear Supertypes
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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
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  7. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  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
    Any

  13. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  14. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  21. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  27. final def notify(): Unit

    Definition Classes
    AnyRef

  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

    Definition Classes
    AnyRef

  34. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

    Definition Classes
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    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

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