org.bdgenomics.adam.rdd

GenomicRegionPartitioner

class GenomicRegionPartitioner extends Partitioner with Logging

GenomicRegionPartitioner 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).

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Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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Instance Constructors

  1. new GenomicRegionPartitioner(numParts: Int, seqDict: SequenceDictionary)

  2. new GenomicRegionPartitioner(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

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

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  6. final def asInstanceOf[T0]: T0

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  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 equals(x: Any): Boolean

    Definition Classes
    GenomicRegionPartitioner → AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. def getPartition(key: Any): Int

    Definition Classes
    GenomicRegionPartitioner → Partitioner

  14. def hashCode(): Int

    Definition Classes
    GenomicRegionPartitioner → AnyRef → Any

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  16. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  17. val lengths: Seq[Long]

  18. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

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    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

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    protected
    Definition Classes
    Logging

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

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    protected
    Definition Classes
    Logging

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

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    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

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    protected
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    Logging

  29. val names: Seq[String]

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

    Definition Classes
    AnyRef

  31. final def notify(): Unit

    Definition Classes
    AnyRef

  32. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  33. def numPartitions: Int

    Definition Classes
    GenomicRegionPartitioner → Partitioner

  34. 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.

  35. 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.

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

    Definition Classes
    AnyRef

  37. def toString(): String

    Definition Classes
    GenomicRegionPartitioner → AnyRef → Any

  38. val totalLength: Long

  39. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    @throws( ... )

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

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    @throws( ... )

Inherited from Logging

Inherited from Partitioner

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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