CompareADAM

Instance Constructors

new CompareADAM(args: CompareADAMArgs)

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
val args: CompareADAMArgs

Attributes
protected
Definition Classes
CompareADAM → BDGSparkCommand
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
val companion: BDGCommandCompanion

Definition Classes
CompareADAM → BDGCommand
final def eq(arg0: AnyRef): Boolean

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

Definition Classes
AnyRef → Any
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 hashCode(): Int

Definition Classes
AnyRef → Any
def initializeMetrics(sc: SparkContext): Option[MetricsListener]

Definition Classes
BDGSparkCommand
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isTraceEnabled(): Boolean

Attributes
protected
Definition Classes
Logging
def log: Logger

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

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

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

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

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

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

Attributes
protected
Definition Classes
Logging
def logName: String

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

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

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

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

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 printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit

Definition Classes
BDGSparkCommand
def printSummary(engine: ComparisonTraversalEngine, generators: Seq[BucketComparisons[Any]], aggregateds: Seq[Histogram[Any]], writer: PrintWriter): Unit

prints out a high-level summary of the compared files, including
prints out a high-level summary of the compared files, including
- the number of reads in each file
- the number of reads which were unique to each file (i.e. not found in the other file, by name)
- for each generator / aggregation created, prints out the total number of reads that went into the aggregation as well as the total which represent "identity" between the compared files (right now, this second number really only makes sense for the Histogram aggregated value, but that's the only aggregator we're using anyway.)
engine
The ComparisonTraversalEngine used for the aggregated values
writer
The PrintWriter to print the summary with.
def run(sc: SparkContext): Unit

Definition Classes
CompareADAM → BDGSparkCommand
def run(): Unit

Definition Classes
BDGSparkCommand → Runnable
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
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( ... )

class CompareADAM extends BDGSparkCommand[CompareADAMArgs] with Serializable

Instance Constructors

new CompareADAM(args: CompareADAMArgs)

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

val args: CompareADAMArgs

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val companion: BDGCommandCompanion

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

def initializeMetrics(sc: SparkContext): Option[MetricsListener]

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 printMetrics(totalTime: Long, metricsListener: Option[MetricsListener]): Unit

def printSummary(engine: ComparisonTraversalEngine, generators: Seq[BucketComparisons[Any]], aggregateds: Seq[Histogram[Any]], writer: PrintWriter): Unit

def run(sc: SparkContext): Unit

def run(): Unit

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 Serializable

Inherited from Serializable

Inherited from BDGSparkCommand[CompareADAMArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped