PartitionedRegionsArgs

Command-line arguments related to partitioning regions according to a LociPartitioning.

Allows for configuring how/whether to persist the computed PartitionedRegions (its RDD of regions and/or its LociPartitioning).

The --partitioning-dir, if present, specifies a location that both read- and loci- partitionings will be saved to; each one can also be set individually via --partitioning-dir and --loci-partitioning.

Linear Supertypes

LociPartitionerArgs, CappedRegionsPartitionerArgs, HalfWindowConfig, MicroRegionPartitionerArgs, UniformPartitionerArgs, AnyRef, Any

Known Subclasses

Arguments, Arguments, Arguments, Arguments, Arguments, PartitionReadsArgs

Value Members

final def !=(arg0: AnyRef): Boolean

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

Definition Classes
Any
final def ##(): Int

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

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

Definition Classes
Any
var _lociPartitioningPathOpt: Option[String]

Attributes
protected
Definition Classes
LociPartitionerArgs
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

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

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
var explodeCoverage: Boolean

Definition Classes
CappedRegionsPartitionerArgs
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 halfWindowSize: Int

Definition Classes
HalfWindowConfig
def hashCode(): Int

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
var lociPartitionerName: String

Attributes
protected
Definition Classes
LociPartitionerArgs
def lociPartitioningPathOpt: Option[String]

Simple getter interface here supports overriding behavior here to support different resolution logic, cf.
Simple getter interface here supports overriding behavior here to support different resolution logic, cf. PartitionedRegionsArgs.

Definition Classes
PartitionedRegionsArgs → LociPartitionerArgs
var maxReadsPerPartition: Int

Definition Classes
CappedRegionsPartitionerArgs
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(sc: SparkContext): Int

Definition Classes
UniformPartitionerArgs
var parallelism: NumPartitions

Attributes
protected
Definition Classes
UniformPartitionerArgs
def partitionedReadsPathOpt: Option[String]
var partitioningAccuracy: NumMicroPartitions

Long >= 1.
Long >= 1. Number of micro-partitions generated for each of the numPartitions Spark partitions that will be computed. Higher values of this will result in a more exact but more expensive computation. In the extreme, setting this to greater than the number of loci (per partition) will result in an exact calculation.

Definition Classes
MicroRegionPartitionerArgs
var printPartitioningStats: Boolean

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

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
var trimRanges: Boolean

Definition Classes
CappedRegionsPartitionerArgs
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( ... )

trait PartitionedRegionsArgs extends LociPartitionerArgs

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

var _lociPartitioningPathOpt: Option[String]

final def asInstanceOf[T0]: T0

def clone(): AnyRef

var compressReadPartitions: Boolean

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

var explodeCoverage: Boolean

def finalize(): Unit

final def getClass(): Class[_]

def halfWindowSize: Int

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

var lociPartitionerName: String

def lociPartitioningPathOpt: Option[String]

var maxReadsPerPartition: Int

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def numPartitions(sc: SparkContext): Int

var parallelism: NumPartitions

def partitionedReadsPathOpt: Option[String]

var partitioningAccuracy: NumMicroPartitions

var printPartitioningStats: Boolean

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

def toString(): String

var trimRanges: Boolean

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from LociPartitionerArgs

Inherited from CappedRegionsPartitionerArgs

Inherited from HalfWindowConfig

Inherited from MicroRegionPartitionerArgs

Inherited from UniformPartitionerArgs

Inherited from AnyRef

Inherited from Any

Ungrouped