org.bdgenomics.adam.rdd

GenomicPositionPartitioner

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.

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Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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  1. GenomicPositionPartitioner
  2. Product
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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

    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
    @throws( ... )
  6. val cumulativeLengths: Map[String, Long]

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

    Definition Classes
    AnyRef
  8. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  10. def getPartition(key: Any): Int

    Definition Classes
    GenomicPositionPartitioner → Partitioner
  11. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  12. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging
  13. val lengths: Seq[Long]

  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. val names: Seq[String]

  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

    Definition Classes
    GenomicPositionPartitioner → Partitioner
  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. val totalLength: Long

  36. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit

    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

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