TransformAlignments

Instance Constructors

new TransformAlignments(args: TransformAlignmentsArgs)

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
def apply(rdd: AlignmentRecordRDD): AlignmentRecordRDD
val args: TransformAlignmentsArgs

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

Definition Classes
Any
def clone(): AnyRef

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

Definition Classes
TransformAlignments → 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] )
def forceNonParquet(): Boolean
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 isNonParquet(inputPath: String): Boolean
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
def maybeMdTag(sc: SparkContext, rdd: AlignmentRecordRDD, stringencyOpt: Option[ValidationStringency]): AlignmentRecordRDD

rdd
The RDD of reads that was output by maybeSort.
stringencyOpt
An optional validation stringency.
returns
If -add_md_tags is set, recomputes the MD tags for the reads provided. If some reads have tags, -md_tag_overwrite controls whether these tags are recomputed or not. If MD tagging isn't requested, we return the input RDD.
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 run(sc: SparkContext): Unit

Definition Classes
TransformAlignments → BDGSparkCommand
def run(): Unit

Definition Classes
BDGSparkCommand → Runnable
val stringency: ValidationStringency
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( ... )

Related Docs: object TransformAlignments | package cli

class TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging

Instance Constructors

new TransformAlignments(args: TransformAlignmentsArgs)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def apply(rdd: AlignmentRecordRDD): AlignmentRecordRDD

val args: TransformAlignmentsArgs

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val companion: TransformAlignments.type

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

def forceNonParquet(): Boolean

final def getClass(): Class[_]

def hashCode(): Int

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

final def isInstanceOf[T0]: Boolean

def isNonParquet(inputPath: String): 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

def maybeMdTag(sc: SparkContext, rdd: AlignmentRecordRDD, stringencyOpt: Option[ValidationStringency]): AlignmentRecordRDD

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

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

def run(sc: SparkContext): Unit

def run(): Unit

val stringency: ValidationStringency

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 BDGSparkCommand[TransformAlignmentsArgs]

Inherited from Logging

Inherited from BDGCommand

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

Ungrouped