Packages

class VariantContextSetBuilder extends Iterable[VariantContext]

A class to make artificial variant contexts and VCFs just a little bit easier to generate.

This builder uses the default sequence dictionary from [SamBuilder] by default.

Linear Supertypes
Iterable[VariantContext], IterableLike[VariantContext, Iterable[VariantContext]], Equals, GenIterable[VariantContext], GenIterableLike[VariantContext, Iterable[VariantContext]], Traversable[VariantContext], GenTraversable[VariantContext], GenericTraversableTemplate[VariantContext, Iterable], TraversableLike[VariantContext, Iterable[VariantContext]], GenTraversableLike[VariantContext, Iterable[VariantContext]], Parallelizable[VariantContext, ParIterable[VariantContext]], TraversableOnce[VariantContext], GenTraversableOnce[VariantContext], FilterMonadic[VariantContext, Iterable[VariantContext]], HasNewBuilder[VariantContext, Iterable[htsjdk.variant.variantcontext.VariantContext] @scala.annotation.unchecked.uncheckedVariance], AnyRef, Any
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Inherited
  1. VariantContextSetBuilder
  2. Iterable
  3. IterableLike
  4. Equals
  5. GenIterable
  6. GenIterableLike
  7. Traversable
  8. GenTraversable
  9. GenericTraversableTemplate
  10. TraversableLike
  11. GenTraversableLike
  12. Parallelizable
  13. TraversableOnce
  14. GenTraversableOnce
  15. FilterMonadic
  16. HasNewBuilder
  17. AnyRef
  18. Any
Implicitly
  1. by MonadOps
  2. by CollectionsHaveToParArray
  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
  7. by alternateImplicit
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new VariantContextSetBuilder(sampleNames: Seq[String] = List("Sample"))

Type Members

  1. type Self = Iterable[VariantContext]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  2. 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 VariantContextSetBuilder to any2stringadd[VariantContextSetBuilder] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: VariantContext, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: VariantContext, That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: VariantContext, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike
  7. def ->[B](y: B): (VariantContextSetBuilder, B)
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to ArrowAssoc[VariantContextSetBuilder] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  8. def /:[B](z: B)(op: (B, VariantContext) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  9. def :\[B](z: B)(op: (VariantContext, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. def addMetaDataLine(headerLine: VCFHeaderLine): VariantContextSetBuilder.this.type

    Adds the header line to the header for this builder.

    Adds the header line to the header for this builder. This should be set before adding variants.

  12. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  13. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  14. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  15. def addVariant(refIdx: Int = 0, start: Long, variantAlleles: List[String], variantAttributes: Map[String, Any] = Map.empty, genotypeAlleles: List[String] = List.empty, genotypeAttributes: Map[String, Any] = Map.empty, sampleName: Option[String] = None, phased: Boolean = false): VariantContextSetBuilder.this.type

    Adds a variant to the builder.

    Adds a variant to the builder.

    If a variant context already exists with the same contig, start, stop, and variant alleles, then we add this genotype to that variant, otherwise we add a new variant and genotype.

    The variant alleles must always be given, as we use them to determine if this variant already exists when adding a genotype for a new sample.

    If no genotype alleles are given, the genotype is a no call.

    If the sample name is not given, the first sample name in the header (in order) is used. There must not already be a genotype for this variant with the given sample name, and the sample name must be present in the header.

  16. def aggregate[B](z: ⇒ B)(seqop: (B, VariantContext) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  17. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  18. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  19. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  20. def collect[B, That](pf: PartialFunction[VariantContext, B])(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  21. def collectFirst[B](pf: PartialFunction[VariantContext, B]): Option[B]
    Definition Classes
    TraversableOnce
  22. def companion: GenericCompanion[Iterable]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  23. def copyToArray[B >: VariantContext](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  24. def copyToArray[B >: VariantContext](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  25. def copyToArray[B >: VariantContext](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  26. def copyToBuffer[B >: VariantContext](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  27. def count(p: (VariantContext) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  28. def drop(n: Int): Iterable[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  29. def dropRight(n: Int): Iterable[VariantContext]
    Definition Classes
    IterableLike
  30. def dropWhile(p: (VariantContext) ⇒ Boolean): Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  31. def ensuring(cond: (VariantContextSetBuilder) ⇒ Boolean, msg: ⇒ Any): VariantContextSetBuilder
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to Ensuring[VariantContextSetBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: (VariantContextSetBuilder) ⇒ Boolean): VariantContextSetBuilder
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to Ensuring[VariantContextSetBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. def ensuring(cond: Boolean, msg: ⇒ Any): VariantContextSetBuilder
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to Ensuring[VariantContextSetBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  34. def ensuring(cond: Boolean): VariantContextSetBuilder
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to Ensuring[VariantContextSetBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  35. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  36. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  37. def exists(p: (VariantContext) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  38. def filter(p: (VariantContext) ⇒ Boolean): Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  39. def filterNot(p: (VariantContext) ⇒ Boolean): Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  40. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  41. def find(p: (VariantContext) ⇒ Boolean): Option[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  42. def flatMap[B, That](f: (VariantContext) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  43. def flatten[B](implicit asTraversable: (VariantContext) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    GenericTraversableTemplate
  44. def fold[A1 >: VariantContext](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  45. def foldLeft[B](z: B)(op: (B, VariantContext) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  46. def foldRight[B](z: B)(op: (VariantContext, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  47. def forall(p: (VariantContext) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  48. def foreach[U](f: (VariantContext) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  49. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to StringFormat[VariantContextSetBuilder] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  50. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  51. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  52. def groupBy[K](f: (VariantContext) ⇒ K): Map[K, Iterable[VariantContext]]
    Definition Classes
    TraversableLike → GenTraversableLike
  53. def grouped(size: Int): Iterator[Iterable[VariantContext]]
    Definition Classes
    IterableLike
  54. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  55. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  56. def head: VariantContext
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  57. def headOption: Option[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  58. def header: VCFHeader
  59. def init: Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  60. def inits: Iterator[Iterable[VariantContext]]
    Definition Classes
    TraversableLike
  61. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  62. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  63. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  64. def iterator: Iterator[VariantContext]

    Gets an iterator over the variants.

    Gets an iterator over the variants.

    Definition Classes
    VariantContextSetBuilder → IterableLike → GenIterableLike
  65. def last: VariantContext
    Definition Classes
    TraversableLike → GenTraversableLike
  66. def lastOption: Option[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  67. def map[B, That](f: (VariantContext) ⇒ B)(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  68. def max[B >: VariantContext](implicit cmp: Ordering[B]): VariantContext
    Definition Classes
    TraversableOnce → GenTraversableOnce
  69. def maxBy[B](f: (VariantContext) ⇒ B)(implicit cmp: Ordering[B]): VariantContext
    Definition Classes
    TraversableOnce → GenTraversableOnce
  70. def min[B >: VariantContext](implicit cmp: Ordering[B]): VariantContext
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def minBy[B](f: (VariantContext) ⇒ B)(implicit cmp: Ordering[B]): VariantContext
    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  73. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  75. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  76. def newBuilder: Builder[VariantContext, Iterable[VariantContext]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  77. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  78. final def notify(): Unit
    Definition Classes
    AnyRef
  79. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  80. def par: ParIterable[VariantContext]
    Definition Classes
    Parallelizable
  81. def parCombiner: Combiner[VariantContext, ParIterable[VariantContext]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  82. def partition(p: (VariantContext) ⇒ Boolean): (Iterable[VariantContext], Iterable[VariantContext])
    Definition Classes
    TraversableLike → GenTraversableLike
  83. def product[B >: VariantContext](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def reduce[A1 >: VariantContext](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def reduceLeft[B >: VariantContext](op: (B, VariantContext) ⇒ B): B
    Definition Classes
    TraversableOnce
  86. def reduceLeftOption[B >: VariantContext](op: (B, VariantContext) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. def reduceOption[A1 >: VariantContext](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  88. def reduceRight[B >: VariantContext](op: (VariantContext, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  89. def reduceRightOption[B >: VariantContext](op: (VariantContext, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. def repr: Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  91. def reversed: List[VariantContext]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  92. def sameElements[B >: VariantContext](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  93. def scan[B >: VariantContext, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  94. def scanLeft[B, That](z: B)(op: (B, VariantContext) ⇒ B)(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  95. def scanRight[B, That](z: B)(op: (VariantContext, B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[VariantContext], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.

  96. def seq: Iterable[VariantContext]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  97. def setHeader(header: VCFHeader): VariantContextSetBuilder.this.type

    Sets the VCF header for this builder.

    Sets the VCF header for this builder. This should be set before adding variants.

  98. def setSequenceDictionary(dict: SAMSequenceDictionary): VariantContextSetBuilder.this.type

    Sets the sequence dictionary for this builder.

    Sets the sequence dictionary for this builder. This should be set before adding variants.

  99. def size: Int

    Returns the number of variants added to this builder.

    Returns the number of variants added to this builder.

    Definition Classes
    VariantContextSetBuilder → GenTraversableLike → TraversableOnce → GenTraversableOnce
  100. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  101. def slice(from: Int, until: Int): Iterable[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  102. def sliding(size: Int, step: Int): Iterator[Iterable[VariantContext]]
    Definition Classes
    IterableLike
  103. def sliding(size: Int): Iterator[Iterable[VariantContext]]
    Definition Classes
    IterableLike
  104. def span(p: (VariantContext) ⇒ Boolean): (Iterable[VariantContext], Iterable[VariantContext])
    Definition Classes
    TraversableLike → GenTraversableLike
  105. def splitAt(n: Int): (Iterable[VariantContext], Iterable[VariantContext])
    Definition Classes
    TraversableLike → GenTraversableLike
  106. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  107. def sum[B >: VariantContext](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  109. def tail: Iterable[VariantContext]
    Definition Classes
    TraversableLike → GenTraversableLike
  110. def tails: Iterator[Iterable[VariantContext]]
    Definition Classes
    TraversableLike
  111. def take(n: Int): Iterable[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  112. def takeRight(n: Int): Iterable[VariantContext]
    Definition Classes
    IterableLike
  113. def takeWhile(p: (VariantContext) ⇒ Boolean): Iterable[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  114. def thisCollection: Iterable[VariantContext]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  115. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, VariantContext, Col[VariantContext]]): Col[VariantContext]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  116. def toArray[B >: VariantContext](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  117. def toBuffer[B >: VariantContext]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  118. def toCollection(repr: Iterable[VariantContext]): Iterable[VariantContext]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  119. def toIndexedSeq: IndexedSeq[VariantContext]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  120. def toIterable: Iterable[VariantContext]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  121. def toIterator: Iterator[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  122. def toList: List[VariantContext]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  123. def toMap[T, U](implicit ev: <:<[VariantContext, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  124. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to CollectionsHaveToParArray[VariantContextSetBuilder, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (VariantContextSetBuilder) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
    CollectionsHaveToParArray
  125. def toSeq: Seq[VariantContext]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  126. def toSet[B >: VariantContext]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  127. def toStream: Stream[VariantContext]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  128. def toString(): String
    Definition Classes
    TraversableLike → Any
  129. def toTempFile(deleteOnExit: Boolean = true): FgBioDef.PathToVcf

    Writes the contents to a temporary file that will be deleted when the JVM exits.

  130. def toTraversable: Traversable[VariantContext]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  131. def toVcfFileReader(deleteOnExit: Boolean = true): VCFFileReader

    Writes the contents to a temporary file that will be deleted when the JVM exits and provides a [VCFFileReader].

  132. def toVector: Vector[VariantContext]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  133. def transpose[B](implicit asTraversable: (VariantContext) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  134. def unzip[A1, A2](implicit asPair: (VariantContext) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
    GenericTraversableTemplate
  135. def unzip3[A1, A2, A3](implicit asTriple: (VariantContext) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
    GenericTraversableTemplate
  136. def view(from: Int, until: Int): IterableView[VariantContext, Iterable[VariantContext]]
    Definition Classes
    IterableLike → TraversableLike
  137. def view: IterableView[VariantContext, Iterable[VariantContext]]
    Definition Classes
    IterableLike → TraversableLike
  138. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  139. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  140. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  141. def withFilter(p: (VariantContext) ⇒ Boolean): FilterMonadic[VariantContext, Iterable[VariantContext]]
    Definition Classes
    TraversableLike → FilterMonadic
  142. def write(path: FgBioDef.PathToVcf): Unit

    Writes the contents of the record set to the provided file path.

  143. def zip[A1 >: VariantContext, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[VariantContext], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  144. def zipAll[B, A1 >: VariantContext, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[VariantContext], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  145. def zipWithIndex[A1 >: VariantContext, That](implicit bf: CanBuildFrom[Iterable[VariantContext], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  146. def →[B](y: B): (VariantContextSetBuilder, B)
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to ArrowAssoc[VariantContextSetBuilder] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: (VariantContext) ⇒ Boolean): TraversableOnce[VariantContext]
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to MonadOps[VariantContext] 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:
    (variantContextSetBuilder: MonadOps[VariantContext]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: (VariantContext) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to MonadOps[VariantContext] 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:
    (variantContextSetBuilder: MonadOps[VariantContext]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: (VariantContext) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to MonadOps[VariantContext] 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:
    (variantContextSetBuilder: MonadOps[VariantContext]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: (VariantContext) ⇒ Boolean): Iterator[VariantContext]
    Implicit
    This member is added by an implicit conversion from VariantContextSetBuilder to MonadOps[VariantContext] 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:
    (variantContextSetBuilder: MonadOps[VariantContext]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from Iterable[VariantContext]

Inherited from IterableLike[VariantContext, Iterable[VariantContext]]

Inherited from Equals

Inherited from GenIterable[VariantContext]

Inherited from GenIterableLike[VariantContext, Iterable[VariantContext]]

Inherited from Traversable[VariantContext]

Inherited from GenTraversable[VariantContext]

Inherited from GenericTraversableTemplate[VariantContext, Iterable]

Inherited from TraversableLike[VariantContext, Iterable[VariantContext]]

Inherited from GenTraversableLike[VariantContext, Iterable[VariantContext]]

Inherited from Parallelizable[VariantContext, ParIterable[VariantContext]]

Inherited from TraversableOnce[VariantContext]

Inherited from GenTraversableOnce[VariantContext]

Inherited from FilterMonadic[VariantContext, Iterable[VariantContext]]

Inherited from HasNewBuilder[VariantContext, Iterable[htsjdk.variant.variantcontext.VariantContext] @scala.annotation.unchecked.uncheckedVariance]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from VariantContextSetBuilder to MonadOps[VariantContext]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from VariantContextSetBuilder to ForceImplicitAmbiguity

Ungrouped