PicardMetricsTask

abstract def in: PathToBam

The path to the input BAM

abstract def metricsExtension: String

All Picard metric generating tools should define their own metrics extension.

final def !=(arg0: Any): Boolean

final def ##(): Int

def +(other: String): String

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

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

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

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

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

def ensuring(cond: Boolean): PicardMetricsTask

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

def formatted(fmtstr: String): String

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def metricsFile(extension: String, kind: PicardOutput.Value): Path

Build a path to a metrics file (text of PDF) using the appropriate prefix derived from either the supplied prefix, or the input file name.

def metricsFile: Path

Gets the metrics file path, assuming that the program generates a single metrics file with a known extension.

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def pathPrefix: PathPrefix

Method that should be used to fetch the file prefix, instead of accessing prefix directly.

def prefix: Option[PathPrefix]

The optional path to the prefix of the metrics file

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

def →[B](y: B): (PicardMetricsTask, B)