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com.fulcrumgenomics.umi.ReviewConsensusVariants

ConsensusVariantReviewInfo

case class ConsensusVariantReviewInfo(chrom: String, pos: Int, ref: String, genotype: String, filters: String, A: Int, C: Int, G: Int, T: Int, N: Int, consensus_read: String, consensus_insert: String, consensus_call: String, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int) extends Metric with Product with Serializable

Detailed information produced by ReviewConsensusVariants on variants called in consensus reads. Each row contains information about a consensus _read_ that carried a variant or non-reference allele at a particular variant site.

The first 10 columns (up to N) contain information about the variant site and are repeated for each consensus read reported at that site. The remaining fields are specific to the consensus read.

chrom

The chromosome on which the variant exists.

pos

The position of the variant.

ref

The reference allele at the position.

genotype

The genotype of the sample in question.

filters

The set of filters applied to the variant in the VCF.

A

The count of A observations at the variant locus across all consensus reads.

C

The count of C observations at the variant locus across all consensus reads.

G

The count of G observations at the variant locus across all consensus reads.

T

The count of T observations at the variant locus across all consensus reads.

N

The count of N observations at the variant locus across all consensus reads.

consensus_read

The consensus read name for which the following fields contain values.

consensus_insert

A description of the insert that generated the consensus read.

consensus_call

The base call from the consensus read.

consensus_qual

The quality score from the consensus read.

a

The number of As in raw-reads contributing to the consensus base call at the variant site.

c

The number of Cs in raw-reads contributing to the consensus base call at the variant site.

g

The number of Gs in raw-reads contributing to the consensus base call at the variant site.

t

The number of Ts in raw-reads contributing to the consensus base call at the variant site.

n

The number of Ns in raw-reads contributing to the consensus base call at the variant site.

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

  1. new ConsensusVariantReviewInfo(chrom: String, pos: Int, ref: String, genotype: String, filters: String, A: Int, C: Int, G: Int, T: Int, N: Int, consensus_read: String, consensus_insert: String, consensus_call: String, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int)

    chrom

    The chromosome on which the variant exists.

    pos

    The position of the variant.

    ref

    The reference allele at the position.

    genotype

    The genotype of the sample in question.

    filters

    The set of filters applied to the variant in the VCF.

    A

    The count of A observations at the variant locus across all consensus reads.

    C

    The count of C observations at the variant locus across all consensus reads.

    G

    The count of G observations at the variant locus across all consensus reads.

    T

    The count of T observations at the variant locus across all consensus reads.

    N

    The count of N observations at the variant locus across all consensus reads.

    consensus_read

    The consensus read name for which the following fields contain values.

    consensus_insert

    A description of the insert that generated the consensus read.

    consensus_call

    The base call from the consensus read.

    consensus_qual

    The quality score from the consensus read.

    a

    The number of As in raw-reads contributing to the consensus base call at the variant site.

    c

    The number of Cs in raw-reads contributing to the consensus base call at the variant site.

    g

    The number of Gs in raw-reads contributing to the consensus base call at the variant site.

    t

    The number of Ts in raw-reads contributing to the consensus base call at the variant site.

    n

    The number of Ns in raw-reads contributing to the consensus base call at the variant site.

Type Members

  1. type Proportion = Double
    Definition Classes
    Metric
  2. type Self = Iterable[(String, String)]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  3. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike

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 ConsensusVariantReviewInfo to any2stringadd[ConsensusVariantReviewInfo] 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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  6. def ++:[B >: (String, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  7. def ->[B](y: B): (ConsensusVariantReviewInfo, B)
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to ArrowAssoc[ConsensusVariantReviewInfo] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
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    @inline()
  8. def /:[B](z: B)(op: (B, (String, String)) ⇒ B): B
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  9. def :\[B](z: B)(op: ((String, String), B) ⇒ B): B
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  10. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. val A: Int
  12. val C: Int
  13. val G: Int
  14. val N: Int
  15. val T: Int
  16. val a: Int
  17. def addString(b: StringBuilder): StringBuilder
    Definition Classes
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  18. def addString(b: StringBuilder, sep: String): StringBuilder
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  19. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
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  20. def aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B
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  21. 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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  22. final def asInstanceOf[T0]: T0
    Definition Classes
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  23. val c: Int
  24. def canEqual(that: Any): Boolean
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  25. val chrom: String
  26. def clone(): AnyRef
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    @throws( ... )
  27. def collect[B, That](pf: PartialFunction[(String, String), B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  28. def collectFirst[B](pf: PartialFunction[(String, String), B]): Option[B]
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  29. def companion: GenericCompanion[Iterable]
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  30. val consensus_call: String
  31. val consensus_insert: String
  32. val consensus_qual: Int
  33. val consensus_read: String
  34. def copyToArray[B >: (String, String)](xs: Array[B], start: Int, len: Int): Unit
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  35. def copyToArray[B >: (String, String)](xs: Array[B]): Unit
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  36. def copyToArray[B >: (String, String)](xs: Array[B], start: Int): Unit
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  37. def copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit
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  38. def count(p: ((String, String)) ⇒ Boolean): Int
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  39. def drop(n: Int): Iterable[(String, String)]
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  40. def dropRight(n: Int): Iterable[(String, String)]
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  41. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  42. def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  43. def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
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  44. def ensuring(cond: Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  45. def ensuring(cond: Boolean): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
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    Ensuring
  46. final def eq(arg0: AnyRef): Boolean
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  47. def exists(p: ((String, String)) ⇒ Boolean): Boolean
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  48. def filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  49. def filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  50. val filters: String
  51. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] )
  52. def find(p: ((String, String)) ⇒ Boolean): Option[(String, String)]
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  53. def flatMap[B, That](f: ((String, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  54. def flatten[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[B]
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  55. def fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1
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  56. def foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
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  57. def foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B
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  58. def forall(p: ((String, String)) ⇒ Boolean): Boolean
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  59. def foreach[U](f: ((String, String)) ⇒ U): Unit
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  60. def formatValues(value: Any): String

    Override this method to customize how values are formatted.

    Override this method to customize how values are formatted.

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    protected
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  61. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to StringFormat[ConsensusVariantReviewInfo] performed by method StringFormat in scala.Predef.
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    @inline()
  62. val g: Int
  63. def genericBuilder[B]: Builder[B, Iterable[B]]
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  64. val genotype: String
  65. def get(name: String): Option[String]

    Gets the value of the field by name, returns None if it does not exist.

    Gets the value of the field by name, returns None if it does not exist.

    Definition Classes
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  66. final def getClass(): Class[_]
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  67. def groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]
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  68. def grouped(size: Int): Iterator[Iterable[(String, String)]]
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  69. def hasDefiniteSize: Boolean
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  70. def head: (String, String)
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  71. def headOption: Option[(String, String)]
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  72. def init: Iterable[(String, String)]
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  73. def inits: Iterator[Iterable[(String, String)]]
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  74. def isEmpty: Boolean
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  75. final def isInstanceOf[T0]: Boolean
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  76. final def isTraversableAgain: Boolean
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  77. def iterator: Iterator[(String, String)]

    Gets an iterator over the fileds of this metric in the order they were defined.

    Gets an iterator over the fileds of this metric in the order they were defined. Returns tuples of names and values

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  78. def last: (String, String)
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  79. def lastOption: Option[(String, String)]
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  80. def map[B, That](f: ((String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  81. def max[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
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  82. def maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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  83. def min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
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  84. def minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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  85. def mkString: String
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  86. def mkString(sep: String): String
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  87. def mkString(start: String, sep: String, end: String): String
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  88. val n: Int
  89. def names: Seq[String]

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

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

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  90. final def ne(arg0: AnyRef): Boolean
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  91. def newBuilder: Builder[(String, String), Iterable[(String, String)]]
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  92. def nonEmpty: Boolean
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  93. final def notify(): Unit
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  94. final def notifyAll(): Unit
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  95. def par: ParIterable[(String, String)]
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  96. def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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  97. def partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  98. val pos: Int
  99. def product[B >: (String, String)](implicit num: Numeric[B]): B
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  100. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
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  101. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
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  102. def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]
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  103. def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]
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  104. def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B
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  105. def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]
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  106. val ref: String
  107. def repr: Iterable[(String, String)]
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  108. def reversed: List[(String, String)]
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  109. def sameElements[B >: (String, String)](that: GenIterable[B]): Boolean
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  110. 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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  111. def scanLeft[B, That](z: B)(op: (B, (String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  112. 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.

  113. def seq: Iterable[(String, String)]
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  114. def size: Int
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  115. def sizeHintIfCheap: Int
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  116. def slice(from: Int, until: Int): Iterable[(String, String)]
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  117. def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
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  118. def sliding(size: Int): Iterator[Iterable[(String, String)]]
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  119. def span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  120. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  121. def stringPrefix: String
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  122. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  123. final def synchronized[T0](arg0: ⇒ T0): T0
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  124. val t: Int
  125. def tail: Iterable[(String, String)]
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  126. def tails: Iterator[Iterable[(String, String)]]
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  127. def take(n: Int): Iterable[(String, String)]
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  128. def takeRight(n: Int): Iterable[(String, String)]
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  129. def takeWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  130. def thisCollection: Iterable[(String, String)]
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  131. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]
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  132. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  133. def toBuffer[B >: (String, String)]: Buffer[B]
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  134. def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]
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  135. def toIndexedSeq: IndexedSeq[(String, String)]
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  136. def toIterable: Iterable[(String, String)]
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  137. def toIterator: Iterator[(String, String)]
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  138. def toList: List[(String, String)]
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  139. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
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  140. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to CollectionsHaveToParArray[ConsensusVariantReviewInfo, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (ConsensusVariantReviewInfo) ⇒ GenTraversableOnce[T] is in scope.
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  141. def toSeq: Seq[(String, String)]
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  142. def toSet[B >: (String, String)]: Set[B]
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  143. def toStream: Stream[(String, String)]
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  144. def toString(): String
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  145. def toTraversable: Traversable[(String, String)]
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  146. def toVector: Vector[(String, String)]
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  147. def transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
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    @migration
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    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  148. def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
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  149. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
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  150. 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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  151. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
    Definition Classes
    IterableLike → TraversableLike
  152. def view: IterableView[(String, String), Iterable[(String, String)]]
    Definition Classes
    IterableLike → TraversableLike
  153. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  154. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  155. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  156. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
    Definition Classes
    TraversableLike → FilterMonadic
  157. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  158. 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
  159. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  160. def [B](y: B): (ConsensusVariantReviewInfo, B)
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to ArrowAssoc[ConsensusVariantReviewInfo] 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 ConsensusVariantReviewInfo 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:
    (consensusVariantReviewInfo: 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 ConsensusVariantReviewInfo 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:
    (consensusVariantReviewInfo: 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 ConsensusVariantReviewInfo 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:
    (consensusVariantReviewInfo: 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 ConsensusVariantReviewInfo 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:
    (consensusVariantReviewInfo: MonadOps[(String, String)]).withFilter(p)
    Definition Classes
    MonadOps

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 ConsensusVariantReviewInfo to MonadOps[(String, String)]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from ConsensusVariantReviewInfo to ForceImplicitAmbiguity

Ungrouped