RodRDDFunctions

Instance Constructors

new RodRDDFunctions(rdd: RDD[Rod])

Value Members

final def !=(arg0: AnyRef): Boolean

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final def !=(arg0: Any): Boolean

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final def ##(): Int

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final def ==(arg0: AnyRef): Boolean

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final def ==(arg0: Any): Boolean

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final def asInstanceOf[T0]: T0

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def clone(): AnyRef

Attributes
protected[java.lang]
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@throws( ... )
def divideRodsBySamples(): RDD[(ReferencePosition, List[Rod])]

Given an RDD of rods, splits the rods up by the specific sample they correspond to.
Given an RDD of rods, splits the rods up by the specific sample they correspond to. Returns an RDD where the samples are grouped by the reference position.
returns
Rods split up by samples and grouped together by position.
final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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def finalize(): Unit

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protected[java.lang]
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@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

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def hashCode(): Int

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final def isInstanceOf[T0]: Boolean

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def isTraceEnabled(): Boolean

Attributes
protected
Definition Classes
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def log: Logger

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protected
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def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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protected
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def logDebug(msg: ⇒ String): Unit

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protected
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def logError(msg: ⇒ String, throwable: Throwable): Unit

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protected
Definition Classes
Logging
def logError(msg: ⇒ String): Unit

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protected
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Logging
def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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protected
Definition Classes
Logging
def logInfo(msg: ⇒ String): Unit

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protected
Definition Classes
Logging
def logName: String

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

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protected
Definition Classes
Logging
def logTrace(msg: ⇒ String): Unit

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

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protected
Definition Classes
Logging
def logWarning(msg: ⇒ String): Unit

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protected
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Logging
final def ne(arg0: AnyRef): Boolean

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final def notify(): Unit

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final def notifyAll(): Unit

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def rodCoverage(): Double

Returns the average coverage for all pileups.
Returns the average coverage for all pileups.
returns
Average coverage across mapped loci.

Note
If running on an RDD with multiple samples where the rods have been split by sample, will return the average coverage per sample, _averaged_ over all samples. If the RDD contains multiple samples and the rods have _not_ been split, this will return the average coverage per sample, _summed_ over all samples.
,
Coverage value does not include locus positions where no reads are mapped, as no rods exist for these positions.
def splitRodsBySamples(): RDD[Rod]

Given an RDD of rods, splits the rods up by the specific sample they correspond to.
Given an RDD of rods, splits the rods up by the specific sample they correspond to. Returns a flat RDD.
returns
Rods split up by samples and _not_ grouped together.
final def synchronized[T0](arg0: ⇒ T0): T0

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def toString(): String

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final def wait(): Unit

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

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@throws( ... )
final def wait(arg0: Long): Unit

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@throws( ... )

class RodRDDFunctions extends Serializable with Logging

Instance Constructors

new RodRDDFunctions(rdd: RDD[Rod])

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

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def divideRodsBySamples(): RDD[(ReferencePosition, List[Rod])]

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def isTraceEnabled(): Boolean

def log: Logger

def logDebug(msg: ⇒ String, throwable: Throwable): Unit

def logDebug(msg: ⇒ String): Unit

def logError(msg: ⇒ String, throwable: Throwable): Unit

def logError(msg: ⇒ String): Unit

def logInfo(msg: ⇒ String, throwable: Throwable): Unit

def logInfo(msg: ⇒ String): Unit

def logName: String

def logTrace(msg: ⇒ String, throwable: Throwable): Unit

def logTrace(msg: ⇒ String): Unit

def logWarning(msg: ⇒ String, throwable: Throwable): Unit

def logWarning(msg: ⇒ String): Unit

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def rodCoverage(): Double

def splitRodsBySamples(): RDD[Rod]

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

def toString(): String

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

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