Packages

case class FamilySizeMetric(family_size: Int, cs_count: Count = 0, cs_fraction: Proportion = 0, cs_fraction_gt_or_eq_size: Proportion = 0, ss_count: Count = 0, ss_fraction: Proportion = 0, ss_fraction_gt_or_eq_size: Proportion = 0, ds_count: Count = 0, ds_fraction: Proportion = 0, ds_fraction_gt_or_eq_size: Proportion = 0) extends Metric with Product with Serializable

Metrics produced by CollectDuplexSeqMetrics to quantify the distribution of different kinds of read family sizes. Three kinds of families are described:

1. _CS_ or _Coordinate & Strand_: families of reads that are grouped together by their unclipped 5' genomic positions and strands just as they are in traditional PCR duplicate marking 2. _SS_ or _Single Strand_: single-strand families that are each subsets of a CS family create by also using the UMIs to partition the larger family, but not linking up families that are created from opposing strands of the same source molecule. 3. _DS_ or _Double Strand_: families that are created by combining single-strand families that are from opposite strands of the same source molecule. This does **not** imply that all DS families are composed of reads from both strands; where only one strand of a source molecule is observed a DS family is still counted.

family_size

The family size, i.e. the number of read pairs grouped together into a family.

cs_count

The count of families with size == family_size when grouping just by coordinates and strand information.

cs_fraction

The fraction of all _CS_ families where size == family_size.

cs_fraction_gt_or_eq_size

The fraction of all _CS_ families where size >= family_size.

ss_count

The count of families with size == family_size when also grouping by UMI to create single-strand families.

ss_fraction

The fraction of all _SS_ families where size == family_size.

ss_fraction_gt_or_eq_size

The fraction of all _SS_ families where size >= family_size.

ds_count

The count of families with size == family_sizewhen also grouping by UMI and merging single-strand families from opposite strands of the same source molecule.

ds_fraction

The fraction of all _DS_ families where size == family_size.

ds_fraction_gt_or_eq_size

The fraction of all _DS_ families where size >= family_size.

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Serializable, Serializable, Metric, Iterable[(String, String)], IterableLike[(String, String), Iterable[(String, String)]], GenIterable[(String, String)], GenIterableLike[(String, String), Iterable[(String, String)]], Traversable[(String, String)], GenTraversable[(String, String)], GenericTraversableTemplate[(String, String), Iterable], TraversableLike[(String, String), Iterable[(String, String)]], GenTraversableLike[(String, String), Iterable[(String, String)]], Parallelizable[(String, String), ParIterable[(String, String)]], TraversableOnce[(String, String)], GenTraversableOnce[(String, String)], FilterMonadic[(String, String), Iterable[(String, String)]], HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance], Product, Equals, AnyRef, Any
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  1. FamilySizeMetric
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Instance Constructors

  1. new FamilySizeMetric(family_size: Int, cs_count: Count = 0, cs_fraction: Proportion = 0, cs_fraction_gt_or_eq_size: Proportion = 0, ss_count: Count = 0, ss_fraction: Proportion = 0, ss_fraction_gt_or_eq_size: Proportion = 0, ds_count: Count = 0, ds_fraction: Proportion = 0, ds_fraction_gt_or_eq_size: Proportion = 0)

    family_size

    The family size, i.e. the number of read pairs grouped together into a family.

    cs_count

    The count of families with size == family_size when grouping just by coordinates and strand information.

    cs_fraction

    The fraction of all _CS_ families where size == family_size.

    cs_fraction_gt_or_eq_size

    The fraction of all _CS_ families where size >= family_size.

    ss_count

    The count of families with size == family_size when also grouping by UMI to create single-strand families.

    ss_fraction

    The fraction of all _SS_ families where size == family_size.

    ss_fraction_gt_or_eq_size

    The fraction of all _SS_ families where size >= family_size.

    ds_count

    The count of families with size == family_sizewhen also grouping by UMI and merging single-strand families from opposite strands of the same source molecule.

    ds_fraction

    The fraction of all _DS_ families where size == family_size.

    ds_fraction_gt_or_eq_size

    The fraction of all _DS_ families where size >= family_size.

Type Members

  1. type Self = Iterable[(String, String)]
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  2. final def ##(): Int
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  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to any2stringadd[FamilySizeMetric] performed by method any2stringadd in scala.Predef.
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  7. def ->[B](y: B): (FamilySizeMetric, B)
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    This member is added by an implicit conversion from FamilySizeMetric to ArrowAssoc[FamilySizeMetric] performed by method ArrowAssoc in scala.Predef.
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  26. def count(p: ((String, String)) ⇒ Boolean): Int
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  27. var cs_count: Count
  28. var cs_fraction: Proportion
  29. var cs_fraction_gt_or_eq_size: Proportion
  30. def drop(n: Int): Iterable[(String, String)]
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  33. var ds_count: Count
  34. var ds_fraction: Proportion
  35. var ds_fraction_gt_or_eq_size: Proportion
  36. def ensuring(cond: (FamilySizeMetric) ⇒ Boolean, msg: ⇒ Any): FamilySizeMetric
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    This member is added by an implicit conversion from FamilySizeMetric to Ensuring[FamilySizeMetric] performed by method Ensuring in scala.Predef.
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  37. def ensuring(cond: (FamilySizeMetric) ⇒ Boolean): FamilySizeMetric
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  38. def ensuring(cond: Boolean, msg: ⇒ Any): FamilySizeMetric
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  39. def ensuring(cond: Boolean): FamilySizeMetric
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  42. val family_size: Int
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  55. def formatted(fmtstr: String): String
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  58. final def getClass(): Class[_]
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    (Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.

  102. def seq: Iterable[(String, String)]
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  109. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  110. var ss_count: Count
  111. var ss_fraction: Proportion
  112. var ss_fraction_gt_or_eq_size: Proportion
  113. def stringPrefix: String
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  114. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  123. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  130. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
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  131. def toParArray: ParArray[T]
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    This member is added by an implicit conversion from FamilySizeMetric to CollectionsHaveToParArray[FamilySizeMetric, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (FamilySizeMetric) ⇒ GenTraversableOnce[T] is in scope.
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  132. def toSeq: Seq[(String, String)]
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  138. def transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
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    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

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  140. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
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  141. def values: Seq[String]

    Get the values of the arguments in the order they were defined.

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  142. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  147. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
    Definition Classes
    TraversableLike → FilterMonadic
  148. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  149. def zipAll[B, A1 >: (String, String), That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  150. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  151. def →[B](y: B): (FamilySizeMetric, B)
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to ArrowAssoc[FamilySizeMetric] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (familySizeMetric: MonadOps[(String, String)]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: ((String, String)) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (familySizeMetric: MonadOps[(String, String)]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: ((String, String)) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (familySizeMetric: MonadOps[(String, String)]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]
    Implicit
    This member is added by an implicit conversion from FamilySizeMetric to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (familySizeMetric: MonadOps[(String, String)]).withFilter(p)
    Definition Classes
    MonadOps

Deprecated Value Members

  1. def formatValues(value: Any): String

    Attributes
    protected
    Definition Classes
    Metric
    Annotations
    @deprecated
    Deprecated

    (Since version 0.5.0) Use formatValue instead.

Inherited from Serializable

Inherited from Serializable

Inherited from Metric

Inherited from Iterable[(String, String)]

Inherited from IterableLike[(String, String), Iterable[(String, String)]]

Inherited from GenIterable[(String, String)]

Inherited from GenIterableLike[(String, String), Iterable[(String, String)]]

Inherited from Traversable[(String, String)]

Inherited from GenTraversable[(String, String)]

Inherited from GenericTraversableTemplate[(String, String), Iterable]

Inherited from TraversableLike[(String, String), Iterable[(String, String)]]

Inherited from GenTraversableLike[(String, String), Iterable[(String, String)]]

Inherited from Parallelizable[(String, String), ParIterable[(String, String)]]

Inherited from TraversableOnce[(String, String)]

Inherited from GenTraversableOnce[(String, String)]

Inherited from FilterMonadic[(String, String), Iterable[(String, String)]]

Inherited from HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance]

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from FamilySizeMetric to MonadOps[(String, String)]

Inherited by implicit conversion CollectionsHaveToParArray from FamilySizeMetric to CollectionsHaveToParArray[FamilySizeMetric, T]

Inherited by implicit conversion any2stringadd from FamilySizeMetric to any2stringadd[FamilySizeMetric]

Inherited by implicit conversion StringFormat from FamilySizeMetric to StringFormat[FamilySizeMetric]

Inherited by implicit conversion Ensuring from FamilySizeMetric to Ensuring[FamilySizeMetric]

Inherited by implicit conversion ArrowAssoc from FamilySizeMetric to ArrowAssoc[FamilySizeMetric]

Inherited by implicit conversion alternateImplicit from FamilySizeMetric to ForceImplicitAmbiguity

Ungrouped