Packages

case class RunInfo(run_barcode: String, flowcell_barcode: String, instrument_name: String, run_date: Iso8601Date, read_structure: ReadStructure, num_lanes: Int) extends Metric with Product with Serializable

Stores the result of parsing the run info (RunInfo.xml) file from an Illumina run folder.

run_barcode

the unique identifier for the sequencing run and flowcell, stored as "<instrument-name>_<flowcell-barcode>".

flowcell_barcode

the flowcell barcode.

instrument_name

the instrument name.

run_date

the date of the sequencing run.

read_structure

the description of the logical structure of cycles within the sequencing run. This will only contain template and sample barcode segments, as the RunInfo.xml does not contain information about other segments (i.e. molecular barcodes and skips).

num_lanes

the number of lanes in the flowcell.

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. RunInfo
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Implicitly
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  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
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Instance Constructors

  1. new RunInfo(run_barcode: String, flowcell_barcode: String, instrument_name: String, run_date: Iso8601Date, read_structure: ReadStructure, num_lanes: Int)

    run_barcode

    the unique identifier for the sequencing run and flowcell, stored as "<instrument-name>_<flowcell-barcode>".

    flowcell_barcode

    the flowcell barcode.

    instrument_name

    the instrument name.

    run_date

    the date of the sequencing run.

    read_structure

    the description of the logical structure of cycles within the sequencing run. This will only contain template and sample barcode segments, as the RunInfo.xml does not contain information about other segments (i.e. molecular barcodes and skips).

    num_lanes

    the number of lanes in the flowcell.

Type Members

  1. type Self = Iterable[(String, String)]
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    protected[this]
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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 RunInfo to any2stringadd[RunInfo] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  5. def ++:[B >: (String, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  7. def ->[B](y: B): (RunInfo, B)
    Implicit
    This member is added by an implicit conversion from RunInfo to ArrowAssoc[RunInfo] 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.

    Gets the value of the field by name.

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  27. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  28. def ensuring(cond: (RunInfo) ⇒ Boolean, msg: ⇒ Any): RunInfo
    Implicit
    This member is added by an implicit conversion from RunInfo to Ensuring[RunInfo] performed by method Ensuring in scala.Predef.
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  29. def ensuring(cond: (RunInfo) ⇒ Boolean): RunInfo
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  30. def ensuring(cond: Boolean, msg: ⇒ Any): RunInfo
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  31. def ensuring(cond: Boolean): RunInfo
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  32. final def eq(arg0: AnyRef): Boolean
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  39. def flatten[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[B]
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  40. val flowcell_barcode: String
  41. def fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1
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  42. def foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
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    Override this method to customize how values are formatted.

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  47. def formatted(fmtstr: String): String
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  48. def genericBuilder[B]: Builder[B, Iterable[B]]
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  49. def get(name: String): Option[String]

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  50. final def getClass(): Class[_]
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  52. def grouped(size: Int): Iterator[Iterable[(String, String)]]
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  53. def hasDefiniteSize: Boolean
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  56. def init: Iterable[(String, String)]
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  57. def inits: Iterator[Iterable[(String, String)]]
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  58. val instrument_name: String
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    Gets an iterator over the fields of this metric in the order they were defined.

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  63. def last: (String, String)
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  72. def mkString(start: String, sep: String, end: String): String
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  73. def names: Seq[String]

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  74. final def ne(arg0: AnyRef): Boolean
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  75. def newBuilder: Builder[(String, String), Iterable[(String, String)]]
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  77. final def notify(): Unit
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  78. final def notifyAll(): Unit
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  79. val num_lanes: Int
  80. def par: ParIterable[(String, String)]
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  81. def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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  82. def partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  83. def product[B >: (String, String)](implicit num: Numeric[B]): B
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  84. val read_structure: ReadStructure
  85. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
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  86. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
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  87. def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]
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  88. def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]
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  89. def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B
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  90. def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]
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  91. def repr: Iterable[(String, String)]
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  92. def reversed: List[(String, String)]
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  93. val run_barcode: String
  94. val run_date: Iso8601Date
  95. def sameElements[B >: (String, String)](that: GenIterable[B]): Boolean
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  96. def scan[B >: (String, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  97. def scanLeft[B, That](z: B)(op: (B, (String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  98. def scanRight[B, That](z: B)(op: ((String, String), B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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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.

  99. def seq: Iterable[(String, String)]
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  100. def size: Int
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  101. def sizeHintIfCheap: Int
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  102. def slice(from: Int, until: Int): Iterable[(String, String)]
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  103. def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
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  104. def sliding(size: Int): Iterator[Iterable[(String, String)]]
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  105. def span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  106. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  107. def stringPrefix: String
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  108. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  109. final def synchronized[T0](arg0: ⇒ T0): T0
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  111. def tails: Iterator[Iterable[(String, String)]]
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  112. def take(n: Int): Iterable[(String, String)]
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  113. def takeRight(n: Int): Iterable[(String, String)]
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  117. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  118. def toBuffer[B >: (String, String)]: Buffer[B]
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  119. def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]
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  123. def toList: List[(String, String)]
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  124. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
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  125. def toParArray: ParArray[T]
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  126. def toSeq: Seq[(String, String)]
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  128. def toStream: Stream[(String, String)]
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  129. def toString(): String
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  130. def toTraversable: Traversable[(String, String)]
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  132. 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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  134. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
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  135. def values: Seq[String]

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  136. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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  137. def view: IterableView[(String, String), Iterable[(String, String)]]
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  138. final def wait(): Unit
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  139. final def wait(arg0: Long, arg1: Int): Unit
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  141. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
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  142. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
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  143. def zipAll[B, A1 >: (String, String), That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
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  144. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
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    This member is added by an implicit conversion from RunInfo 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:
    (runInfo: 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 RunInfo 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:
    (runInfo: 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 RunInfo to CollectionsHaveToParArray[RunInfo, T]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from RunInfo to ForceImplicitAmbiguity

Ungrouped