case class GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true) extends Partitioner with Logging with Product with Serializable

A partitioner for ReferenceRegion-keyed data.

partitionSize

The number of bases per partition.

seqLengths

A map between contig names and contig lengths.

start

If true, use the start position (instead of the end position) to decide which partition a key belongs to.

Linear Supertypes
Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
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  1. GenomicRegionPartitioner
  2. Product
  3. Equals
  4. Logging
  5. Partitioner
  6. Serializable
  7. Serializable
  8. AnyRef
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Instance Constructors

  1. new GenomicRegionPartitioner(partitionSize: Long, seqLengths: Map[String, Long], start: Boolean = true)

    partitionSize

    The number of bases per partition.

    seqLengths

    A map between contig names and contig lengths.

    start

    If true, use the start position (instead of the end position) to decide which partition a key belongs to.

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
    @native() @throws( ... )
  6. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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    protected
    Definition Classes
    Logging
  7. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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    protected
    Definition Classes
    Logging
  8. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  9. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  10. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  11. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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    protected
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  12. def error(msg: ⇒ Any): Unit
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    protected
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  13. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  14. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  15. def getPartition(key: Any): Int

    key

    The key to get the partition index for.

    returns

    The partition that a key should map to.

    Definition Classes
    GenomicRegionPartitioner → Partitioner
    Exceptions thrown

    IllegalArgumentException Throws an exception if the data is not a ReferenceRegion or a tuple of (ReferenceRegion, _).

  16. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  17. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
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    protected
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    Logging
  18. def info(msg: ⇒ Any): Unit
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    protected
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  19. def isDebugEnabled: Boolean
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    protected
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  20. def isErrorEnabled: Boolean
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  21. def isInfoEnabled: Boolean
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    protected
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  22. final def isInstanceOf[T0]: Boolean
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    Any
  23. def isTraceEnabled: Boolean
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    protected
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    Logging
  24. def isWarnEnabled: Boolean
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    Logging
  25. def logger: Logger
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    Logging
  26. def loggerName: String
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    protected
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    Logging
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  30. def numPartitions: Int

    returns

    The number of partitions described by this partitioner. Roughly the size of the genome divided by the partition length.

    Definition Classes
    GenomicRegionPartitioner → Partitioner
  31. val partitionSize: Long
  32. val seqLengths: Map[String, Long]
  33. val start: Boolean
  34. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  35. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
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    Logging
  36. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
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    protected
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  37. def trace(msg: ⇒ Any): Unit
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  38. final def wait(): Unit
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    @throws( ... )
  39. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  40. final def wait(arg0: Long): Unit
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    @native() @throws( ... )
  41. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
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    Logging
  43. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging

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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