Packages

case class DuplexUmiMetric(umi: String, raw_observations: Count = 0, raw_observations_with_errors: Count = 0, unique_observations: Count = 0, fraction_raw_observations: Proportion = 0, fraction_unique_observations: Proportion = 0, fraction_unique_observations_expected: Proportion = 0) extends Metric with Product with Serializable

Metrics produced by CollectDuplexSeqMetrics describing the set of observed duplex UMI sequences and the frequency of their observations. The UMI sequences reported may have been corrected using information within a double-stranded tag family. For example if a tag family is comprised of three read pairs with UMIs ACGT-TGGT, ACGT-TGGT, and ACGT-TGGG then a consensus UMI of ACGT-TGGT will be generated.

UMI pairs are normalized within a tag family so that observations are always reported as if they came from a read pair with read 1 on the positive strand (F1R2). Another way to view this is that for FR or RF read pairs, the duplex UMI reported is the UMI from the positive strand read followed by the UMI from the negative strand read. E.g. a read pair with UMI AAAA-GGGG and with R1 on the negative strand and R2 on the positive strand, will be reported as GGGG-AAAA.

umi

The duplex UMI sequence, possibly-corrected.

raw_observations

The number of read pairs in the input BAM that observe the duplex UMI (after correction).

raw_observations_with_errors

The subset of raw observations that underwent any correction.

unique_observations

The number of double-stranded tag families (i.e unique double-stranded molecules) that observed the duplex UMI.

fraction_raw_observations

The fraction of all raw observations that the duplex UMI accounts for.

fraction_unique_observations

The fraction of all unique observations that the duplex UMI accounts for.

fraction_unique_observations_expected

The fraction of all unique observations that are expected to be attributed to the duplex UMI based on the fraction_unique_observations of the two individual UMIs.

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  1. DuplexUmiMetric
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Instance Constructors

  1. new DuplexUmiMetric(umi: String, raw_observations: Count = 0, raw_observations_with_errors: Count = 0, unique_observations: Count = 0, fraction_raw_observations: Proportion = 0, fraction_unique_observations: Proportion = 0, fraction_unique_observations_expected: Proportion = 0)

    umi

    The duplex UMI sequence, possibly-corrected.

    raw_observations

    The number of read pairs in the input BAM that observe the duplex UMI (after correction).

    raw_observations_with_errors

    The subset of raw observations that underwent any correction.

    unique_observations

    The number of double-stranded tag families (i.e unique double-stranded molecules) that observed the duplex UMI.

    fraction_raw_observations

    The fraction of all raw observations that the duplex UMI accounts for.

    fraction_unique_observations

    The fraction of all unique observations that the duplex UMI accounts for.

    fraction_unique_observations_expected

    The fraction of all unique observations that are expected to be attributed to the duplex UMI based on the fraction_unique_observations of the two individual UMIs.

Type Members

  1. type Self = Iterable[(String, String)]
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  3. def +(other: String): String
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    This member is added by an implicit conversion from DuplexUmiMetric to any2stringadd[DuplexUmiMetric] 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): (DuplexUmiMetric, B)
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    This member is added by an implicit conversion from DuplexUmiMetric to ArrowAssoc[DuplexUmiMetric] performed by method ArrowAssoc in scala.Predef.
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  30. def ensuring(cond: (DuplexUmiMetric) ⇒ Boolean, msg: ⇒ Any): DuplexUmiMetric
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    This member is added by an implicit conversion from DuplexUmiMetric to Ensuring[DuplexUmiMetric] performed by method Ensuring in scala.Predef.
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  31. def ensuring(cond: (DuplexUmiMetric) ⇒ Boolean): DuplexUmiMetric
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    This member is added by an implicit conversion from DuplexUmiMetric to Ensuring[DuplexUmiMetric] performed by method Ensuring in scala.Predef.
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  32. def ensuring(cond: Boolean, msg: ⇒ Any): DuplexUmiMetric
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    This member is added by an implicit conversion from DuplexUmiMetric to Ensuring[DuplexUmiMetric] performed by method Ensuring in scala.Predef.
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  33. def ensuring(cond: Boolean): DuplexUmiMetric
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    This member is added by an implicit conversion from DuplexUmiMetric to Ensuring[DuplexUmiMetric] performed by method Ensuring in scala.Predef.
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  34. final def eq(arg0: AnyRef): Boolean
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  48. def formatted(fmtstr: String): String
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  49. var fraction_raw_observations: Proportion
  50. var fraction_unique_observations: Proportion
  51. var fraction_unique_observations_expected: Proportion
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  54. final def getClass(): Class[_]
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  85. def product[B >: (String, String)](implicit num: Numeric[B]): B
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  86. var raw_observations: Count
  87. var raw_observations_with_errors: Count
  88. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
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  126. def toParArray: ParArray[T]
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    This member is added by an implicit conversion from DuplexUmiMetric to CollectionsHaveToParArray[DuplexUmiMetric, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (DuplexUmiMetric) ⇒ GenTraversableOnce[T] is in scope.
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    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  134. val umi: String
  135. var unique_observations: Count
  136. def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
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  138. def values: Seq[String]

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  139. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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    Definition Classes
    IterableLike → GenIterableLike
  147. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  148. def →[B](y: B): (DuplexUmiMetric, B)
    Implicit
    This member is added by an implicit conversion from DuplexUmiMetric to ArrowAssoc[DuplexUmiMetric] 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 DuplexUmiMetric 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:
    (duplexUmiMetric: 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 DuplexUmiMetric 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:
    (duplexUmiMetric: 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 DuplexUmiMetric 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:
    (duplexUmiMetric: 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 DuplexUmiMetric 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:
    (duplexUmiMetric: 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 DuplexUmiMetric to MonadOps[(String, String)]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from DuplexUmiMetric to ForceImplicitAmbiguity

Ungrouped