GenomicPositionPartitioner

Instance Constructors

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

final def !=(arg0: Any): Boolean

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

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

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

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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protected
Definition Classes
Logging
def debug(msg: ⇒ Any): Unit

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protected
Definition Classes
Logging
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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protected
Definition Classes
Logging
def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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protected
Definition Classes
Logging
def error(msg: ⇒ Any): Unit

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protected
Definition Classes
Logging
def finalize(): Unit

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

Definition Classes
AnyRef → Any
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.
def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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protected
Definition Classes
Logging
def info(msg: ⇒ Any): Unit

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protected
Definition Classes
Logging
def isDebugEnabled: Boolean

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protected
Definition Classes
Logging
def isErrorEnabled: Boolean

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protected
Definition Classes
Logging
def isInfoEnabled: Boolean

Attributes
protected
Definition Classes
Logging
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isTraceEnabled: Boolean

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protected
Definition Classes
Logging
def isWarnEnabled: Boolean

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protected
Definition Classes
Logging
def logger: Logger

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protected
Definition Classes
Logging
def loggerName: String

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

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
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
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.
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.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
GenomicPositionPartitioner → AnyRef → Any
def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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protected
Definition Classes
Logging
def trace(msg: ⇒ Any): Unit

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protected
Definition Classes
Logging
final def wait(): Unit

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

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

Definition Classes
AnyRef
Annotations
@throws( ... )
def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def warn(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging

Related Docs: object GenomicPositionPartitioner | package rdd

case class GenomicPositionPartitioner(numParts: Int, seqLengths: Map[String, Long]) extends Partitioner with Logging with Product with Serializable

Instance Constructors

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

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

def debug(msg: ⇒ Any): Unit

final def eq(arg0: AnyRef): Boolean

def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

def error(msg: ⇒ Any): Unit

def finalize(): Unit

final def getClass(): Class[_]

def getPartition(key: Any): Int

def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

def info(msg: ⇒ Any): Unit

def isDebugEnabled: Boolean

def isErrorEnabled: Boolean

def isInfoEnabled: Boolean

final def isInstanceOf[T0]: Boolean

def isTraceEnabled: Boolean

def isWarnEnabled: Boolean

def logger: Logger

def loggerName: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def numPartitions: Int

val numParts: Int

val seqLengths: Map[String, Long]

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

def toString(): String

def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

def trace(msg: ⇒ Any): Unit

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

def warn(msg: ⇒ Any): Unit

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