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.

Linear Supertypes
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. class WithFilter extends FilterMonadic[A, Repr]
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  1. final def !=(arg0: Any): Boolean
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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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  4. def ++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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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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  8. final def ==(arg0: Any): Boolean
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  13. def apply(name: String): String

    Gets the value of the field by name.

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  24. def count(p: ((String, String)) ⇒ Boolean): Int
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  25. var cs_count: Count
  26. var cs_fraction: Proportion
  27. var cs_fraction_gt_or_eq_size: Proportion
  28. def drop(n: Int): Iterable[(String, String)]
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  29. def dropRight(n: Int): Iterable[(String, String)]
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  31. var ds_count: Count
  32. var ds_fraction: Proportion
  33. var ds_fraction_gt_or_eq_size: Proportion
  34. 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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  35. def ensuring(cond: (FamilySizeMetric) ⇒ Boolean): 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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  36. def ensuring(cond: 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: Boolean): 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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  38. final def eq(arg0: AnyRef): Boolean
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  39. def exists(p: ((String, String)) ⇒ Boolean): Boolean
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  40. val family_size: Int
  41. def filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  42. def filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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    Override this method to customize how values are formatted.

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  53. def formatted(fmtstr: String): String
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  54. def genericBuilder[B]: Builder[B, Iterable[B]]
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  56. final def getClass(): Class[_]
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  57. def groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]
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  58. def grouped(size: Int): Iterator[Iterable[(String, String)]]
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  63. def inits: Iterator[Iterable[(String, String)]]
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  67. def iterator: Iterator[(String, String)]

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  74. def minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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  75. def mkString: String
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  77. def mkString(start: String, sep: String, end: String): String
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  78. def names: Seq[String]

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

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  79. final def ne(arg0: AnyRef): Boolean
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  80. def newBuilder: Builder[(String, String), Iterable[(String, String)]]
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  85. def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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  89. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
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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.

  100. def seq: Iterable[(String, String)]
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  101. def size: Int
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  102. def sizeHintIfCheap: Int
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  103. def slice(from: Int, until: Int): Iterable[(String, String)]
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  104. def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
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  107. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  108. var ss_count: Count
  109. var ss_fraction: Proportion
  110. var ss_fraction_gt_or_eq_size: Proportion
  111. def stringPrefix: String
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  112. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  113. final def synchronized[T0](arg0: ⇒ T0): T0
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  115. def tails: Iterator[Iterable[(String, String)]]
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  116. def take(n: Int): Iterable[(String, String)]
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  119. def thisCollection: Iterable[(String, String)]
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  120. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]
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  121. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  122. def toBuffer[B >: (String, String)]: Buffer[B]
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  123. def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]
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  124. def toIndexedSeq: IndexedSeq[(String, String)]
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  125. def toIterable: Iterable[(String, String)]
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  127. def toList: List[(String, String)]
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  128. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
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  129. def toParArray: ParArray[T]
    Implicit
    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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  130. def toSeq: Seq[(String, String)]
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  131. def toSet[B >: (String, String)]: Set[B]
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  132. def toStream: Stream[(String, String)]
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  133. def toString(): String
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  134. def toTraversable: Traversable[(String, String)]
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  135. def toVector: Vector[(String, String)]
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  136. 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.

  137. def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
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  138. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
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  139. def values: Seq[String]

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

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

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  140. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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  141. def view: IterableView[(String, String), Iterable[(String, String)]]
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  142. final def wait(): Unit
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  143. final def wait(arg0: Long, arg1: Int): Unit
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  145. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
    Definition Classes
    TraversableLike → FilterMonadic
  146. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  147. 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
  148. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  149. 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 /:[B](z: B)(op: (B, (String, String)) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldLeft instead of /:

  2. def :\[B](z: B)(op: ((String, String), B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldRight instead of :\

  3. 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 CollectionsHaveToParArray from FamilySizeMetric to CollectionsHaveToParArray[FamilySizeMetric, T]

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

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