FgBioTask

abstract def addFgBioArgs(buffer: ListBuffer[Any]): Unit

Implement this to add the tool-specific arguments

final def !=(arg0: Any): Boolean

def !=>(other: Dependable): Unit

final def ##(): Int

def +(other: String): String

def ->[B](y: B): (FgBioTask, B)

def ::(other: Option[Dependable]): Dependable

def ::(other: Dependable): Dependable

final def ==(arg0: Any): Boolean

final def ==>(other: Option[Dependable]): Dependable

final def ==>(other: Dependable): Dependable

def addDependent(dependent: Dependable): Unit

def allTasks: Traversable[Task]

def applyResources(resources: ResourceSet): Unit

final def args: Seq[Any]

final def asInstanceOf[T0]: T0

def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

def clone(): AnyRef

def commandLineName(name: String): String

lazy val commandName: String

Looks up the first super class that does not have "$anon$" in its name.

var compressionLevel: Option[Int]

the compress level to use for HTSJDK.

def config: Config

def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

def configureExecutable(path: String, executable: String): Path

def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

def ensuring(cond: (FgBioTask) ⇒ Boolean, msg: ⇒ Any): FgBioTask

def ensuring(cond: (FgBioTask) ⇒ Boolean): FgBioTask

def ensuring(cond: Boolean, msg: ⇒ Any): FgBioTask

def ensuring(cond: Boolean): FgBioTask

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def fgBioJar: Path

Can be overridden to use a specific FgBio jar.

def finalize(): Unit

def formatted(fmtstr: String): String

final def getClass(): Class[_]

final def getTasks: Traversable[_ <: FgBioTask.this.type]

def hashCode(): Int

def headTasks: Traversable[Task]

final def isInstanceOf[T0]: Boolean

def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

lazy val logger: Logger

var name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def onComplete(exitCode: Int): Boolean

def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

def pickResources(availableResources: ResourceSet): Option[ResourceSet]

var quoteIfNecessary: Boolean

def removeDependency(task: Task): Boolean

def requires(cores: Double, memory: String): FgBioTask.this.type

def requires(cores: Cores, memory: Memory): FgBioTask.this.type

def requires(resources: ResourceSet): FgBioTask.this.type

def resources: ResourceSet

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

def systemPath: Seq[Path]

def tailTasks: Traversable[Task]

def tasksDependedOn: Traversable[Task]

def tasksDependingOnThisTask: Traversable[Task]

def toString(): String

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def withCompression(i: Int): FgBioTask.this.type

Sets the compression level to a specific value.

def withName(name: String): FgBioTask.this.type

def →[B](y: B): (FgBioTask, B)