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: 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
    Any

  7. def clone(): AnyRef

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

  8. val cumulativeLengths: Map[String, Long]

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

    Definition Classes
    AnyRef

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. def getPartition(key: Any): Int

    Definition Classes
    GenomicPositionPartitioner → Partitioner

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  14. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  15. val lengths: Seq[Long]

  16. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  23. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  28. val names: Seq[String]

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

    Definition Classes
    AnyRef

  30. final def notify(): Unit

    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  32. def numPartitions: Int

    Definition Classes
    GenomicPositionPartitioner → Partitioner

  33. 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.

  34. 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.

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

    Definition Classes
    AnyRef

  36. def toString(): String

    Definition Classes
    GenomicPositionPartitioner → AnyRef → Any

  37. val totalLength: Long

  38. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  40. 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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