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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  6. Serializable
  7. Serializable
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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
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. final def asInstanceOf[T0]: T0
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  5. def clone(): AnyRef
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    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  6. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  7. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  8. def debug(msg: ⇒ Any): Unit
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  9. final def eq(arg0: AnyRef): Boolean
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  10. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  11. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  12. def error(msg: ⇒ Any): Unit
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  13. final def getClass(): Class[_]
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    @native() @HotSpotIntrinsicCandidate()
  14. 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.

  15. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  16. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  17. def info(msg: ⇒ Any): Unit
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  18. def isDebugEnabled: Boolean
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  19. def isErrorEnabled: Boolean
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  20. def isInfoEnabled: Boolean
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  21. final def isInstanceOf[T0]: Boolean
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  22. def isTraceEnabled: Boolean
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  23. def isWarnEnabled: Boolean
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  24. def logger: Logger
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  25. def loggerName: String
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  26. final def ne(arg0: AnyRef): Boolean
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  27. final def notify(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  28. final def notifyAll(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  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
  31. val seqLengths: Map[String, Long]
  32. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  33. def toString(): String
    Definition Classes
    GenomicPositionPartitioner → AnyRef → Any
  34. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  35. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  36. def trace(msg: ⇒ Any): Unit
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  37. final def wait(arg0: Long, arg1: Int): Unit
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  38. final def wait(arg0: Long): Unit
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  39. final def wait(): Unit
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  40. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  41. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  42. def warn(msg: ⇒ Any): Unit
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Deprecated Value Members

  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from Product

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Inherited from Partitioner

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