GenomicRegionPartitioner

Instance Constructors

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

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

Attributes
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

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

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

Attributes
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

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

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

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

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protected
Definition Classes
Logging
def isDebugEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isErrorEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isInfoEnabled: Boolean

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

Definition Classes
Any
def isTraceEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isWarnEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def logger: Logger

Attributes
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

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

Definition Classes
GenomicRegionPartitioner → Partitioner
val partitionSize: Long

The number of bases per partition.
val seqLengths: Map[String, Long]

A map between contig names and contig lengths.
val start: Boolean

If true, use the start position (instead of the end position) to decide which partition a key belongs to.
final def synchronized[T0](arg0: ⇒ T0): T0

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

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

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

Attributes
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 GenomicRegionPartitioner | package rdd

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

Instance Constructors

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

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 partitionSize: Long

val seqLengths: Map[String, Long]

val start: Boolean

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

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