Class/Object

org.bdgenomics.adam.rdd

GenomicPositionPartitioner

Related Docs: object GenomicPositionPartitioner | package rdd

Permalink

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.

Linear Supertypes
Product, Equals, Logging, Partitioner, Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. GenomicPositionPartitioner
  2. Product
  3. Equals
  4. Logging
  5. Partitioner
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long])

    Permalink

    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

    Permalink
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any
  5. def clone(): AnyRef

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  7. def finalize(): Unit

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  8. final def getClass(): Class[_]

    Permalink
    Definition Classes
    AnyRef → Any
  9. def getPartition(key: Any): Int

    Permalink

    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.

  10. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any
  11. def isTraceEnabled(): Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  12. def log: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  13. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  14. def logDebug(msg: ⇒ String): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  15. def logError(msg: ⇒ String, throwable: Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  16. def logError(msg: ⇒ String): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  17. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  18. def logInfo(msg: ⇒ String): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  19. def logName: String

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  20. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  21. def logTrace(msg: ⇒ String): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  22. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  23. def logWarning(msg: ⇒ String): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    Logging
  24. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  25. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef
  26. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef
  27. def numPartitions: Int

    Permalink

    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

  28. val numParts: Int

    Permalink

    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.

  29. val seqLengths: Map[String, Long]

    Permalink

    a map relating sequence-name to length and indicating the set and length of all extant sequences in the genome.

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

    Permalink
    Definition Classes
    AnyRef
  31. def toString(): String

    Permalink
    Definition Classes
    GenomicPositionPartitioner → AnyRef → Any
  32. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. final def wait(arg0: Long, arg1: Int): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long): Unit

    Permalink
    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

Ungrouped