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
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  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
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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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    protected[java.lang]
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    Annotations
    @throws( ... )

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

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  9. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  11. def getPartition(key: Any): Int

    Computes the partition for a key.

    Computes the partition for a key.

    key

    A key to compute the partition for.

    returns

    The partition that this key belongs to.

    Definition Classes
    GenomicPositionPartitioner → Partitioner
    Exceptions thrown
    IllegalArgumentException

    if the key is not a ReferencePosition, or (ReferencePosition, _) tuple.

  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

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    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

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    protected
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    Logging

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

    Attributes
    protected
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    Logging

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

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    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
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    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

    This is the total number of partitions for both mapped and unmapped positions.

    This is the total number of partitions for both mapped and unmapped positions. All unmapped positions go into the last partition.

    Definition Classes
    GenomicPositionPartitioner → Partitioner
    See also

    parts

  30. 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.

  31. 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.

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

    Definition Classes
    AnyRef

  33. def toString(): String

    Definition Classes
    GenomicPositionPartitioner → AnyRef → Any

  34. final def wait(): Unit

    Definition Classes
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    Annotations
    @throws( ... )

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

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    @throws( ... )

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

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    @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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