Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

   AnyRef → Any

3.  def +(other: String): String

   Implicit

   This member is added by an implicit conversion from CollectDuplexSeqMetrics to any2stringadd[CollectDuplexSeqMetrics] performed by method any2stringadd in scala.Predef.

   Definition Classes

   any2stringadd

4.  def ->[B](y: B): (CollectDuplexSeqMetrics, B)

   Implicit

   This member is added by an implicit conversion from CollectDuplexSeqMetrics to ArrowAssoc[CollectDuplexSeqMetrics] performed by method ArrowAssoc in scala.Predef.

   Definition Classes

   ArrowAssoc

   Annotations

   @inline()

5.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

6.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

8.  def collect(iterator: Iterator[SamRecord]): Unit

   Consumes from the iterator and collects information internally from which to generate metrics.

9.  val description: Option[String]
10.  def duplexFamilySizeMetrics: Seq[DuplexFamilySizeMetric]

    Generates the duplex family size metrics from the current observations.

11.  val duplexUmiCounts: Boolean
12.  def duplexUmiMetrics(umiMetrics: Seq[UmiMetric]): Seq[DuplexUmiMetric]

    Generates the duplex UMI metrics from the current observations.

13.  def ensuring(cond: (CollectDuplexSeqMetrics) ⇒ Boolean, msg: ⇒ Any): CollectDuplexSeqMetrics

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

14.  def ensuring(cond: (CollectDuplexSeqMetrics) ⇒ Boolean): CollectDuplexSeqMetrics

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

15.  def ensuring(cond: Boolean, msg: ⇒ Any): CollectDuplexSeqMetrics

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

16.  def ensuring(cond: Boolean): CollectDuplexSeqMetrics

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to Ensuring[CollectDuplexSeqMetrics] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

17.  final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

18.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

19.  def execute(): Unit

    Definition Classes

    CollectDuplexSeqMetrics → FgBioTool

20.  def fail(exit: Int, message: String): Nothing

    Fail with a specific error code and message.

    Fail with a specific error code and message.

    Definition Classes

    FgBioTool

21.  def fail(message: String): Nothing

    Fail with the default exit code and a message.

    Fail with the default exit code and a message.

    Definition Classes

    FgBioTool

22.  def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes

    FgBioTool

23.  def familySizeMetrics: Seq[FamilySizeMetric]

    Generates the family size metrics from the current observations.

24.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

25.  def formatted(fmtstr: String): String

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to StringFormat[CollectDuplexSeqMetrics] performed by method StringFormat in scala.Predef.

    Definition Classes

    StringFormat

    Annotations

    @inline()

26.  final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

27.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

28.  val input: FgBioDef.PathToBam
29.  val intervals: Option[FgBioDef.PathToIntervals]
30.  def invalid(message: String): Nothing

    Generates a new validation exception with the given message.

    Generates a new validation exception with the given message.

    Definition Classes

    FgBioTool

31.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

32.  lazy val logger: Logger

    Attributes

    protected

    Definition Classes

    LazyLogging

33.  val minAbReads: Int
34.  val minBaReads: Int
35.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

36.  final def notify(): Unit

    Definition Classes

    AnyRef

37.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

38.  val output: FgBioDef.PathPrefix
39.  def pDuplexIdeal(reads: Int): Double

    For a given family size/number of reads computes the probability that we would observed at least minAb & minBa reads under a binomial sampling model with p=0.5.

40.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

41.  def toString(): String

    Definition Classes

    AnyRef → Any

42.  def umiMetrics: Seq[UmiMetric]

    Generates the UMI metrics from the current observations.

43.  def validate(test: Boolean, message: ⇒ String): Unit

    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes

    FgBioTool

44.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

46.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

47.  def yieldMetrics: Seq[DuplexYieldMetric]

    Generates the duplex yield metrics from the current observations.

48.  def →[B](y: B): (CollectDuplexSeqMetrics, B)

    Implicit

    This member is added by an implicit conversion from CollectDuplexSeqMetrics to ArrowAssoc[CollectDuplexSeqMetrics] performed by method ArrowAssoc in scala.Predef.

    Definition Classes

    ArrowAssoc