class RefFlatSource extends Iterable[Gene] with Closeable with LazyLogging

Reads gene annotation information from a RefFlat file.

Skips genes on unrecognized chromosomes if a sequence dictionary is provided.

The format is described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat

A Picard-style header is also supported (GENE_NAME, TRANSCRIPT_NAME, ...).

Linear Supertypes
LazyLogging, Closeable, AutoCloseable, Iterable[Gene], IterableLike[Gene, Iterable[Gene]], Equals, GenIterable[Gene], GenIterableLike[Gene, Iterable[Gene]], Traversable[Gene], GenTraversable[Gene], GenericTraversableTemplate[Gene, Iterable], TraversableLike[Gene, Iterable[Gene]], GenTraversableLike[Gene, Iterable[Gene]], Parallelizable[Gene, ParIterable[Gene]], TraversableOnce[Gene], GenTraversableOnce[Gene], FilterMonadic[Gene, Iterable[Gene]], HasNewBuilder[Gene, Iterable[com.fulcrumgenomics.util.GeneAnnotations.Gene] @scala.annotation.unchecked.uncheckedVariance], AnyRef, Any
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Inherited
  1. RefFlatSource
  2. LazyLogging
  3. Closeable
  4. AutoCloseable
  5. Iterable
  6. IterableLike
  7. Equals
  8. GenIterable
  9. GenIterableLike
  10. Traversable
  11. GenTraversable
  12. GenericTraversableTemplate
  13. TraversableLike
  14. GenTraversableLike
  15. Parallelizable
  16. TraversableOnce
  17. GenTraversableOnce
  18. FilterMonadic
  19. HasNewBuilder
  20. AnyRef
  21. Any
Implicitly
  1. by MonadOps
  2. by CollectionsHaveToParArray
  3. by flattenTraversableOnce
  4. by any2stringadd
  5. by StringFormat
  6. by Ensuring
  7. by ArrowAssoc
  8. by alternateImplicit
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Visibility
  1. Public
  2. All

Type Members

  1. type Self = Iterable[Gene]
    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 RefFlatSource to any2stringadd[RefFlatSource] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: Gene, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: Gene, That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: Gene, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike
  7. def ->[B](y: B): (RefFlatSource, B)
    Implicit
    This member is added by an implicit conversion from RefFlatSource to ArrowAssoc[RefFlatSource] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  8. def /:[B](z: B)(op: (B, Gene) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  9. def :\[B](z: B)(op: (Gene, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  12. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  13. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  14. def aggregate[B](z: ⇒ B)(seqop: (B, Gene) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  15. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  16. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  17. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. def close(): Unit

    Closes the underlying reader; only necessary if EOF hasn't been reached.

    Closes the underlying reader; only necessary if EOF hasn't been reached.

    Definition Classes
    RefFlatSource → Closeable → AutoCloseable
  19. def collect[B, That](pf: PartialFunction[Gene, B])(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  20. def collectFirst[B](pf: PartialFunction[Gene, B]): Option[B]
    Definition Classes
    TraversableOnce
  21. def companion: GenericCompanion[Iterable]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  22. def copyToArray[B >: Gene](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  23. def copyToArray[B >: Gene](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  24. def copyToArray[B >: Gene](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  25. def copyToBuffer[B >: Gene](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  26. def count(p: (Gene) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  27. def drop(n: Int): Iterable[Gene]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  28. def dropRight(n: Int): Iterable[Gene]
    Definition Classes
    IterableLike
  29. def dropWhile(p: (Gene) ⇒ Boolean): Iterable[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  30. def ensuring(cond: (RefFlatSource) ⇒ Boolean, msg: ⇒ Any): RefFlatSource
    Implicit
    This member is added by an implicit conversion from RefFlatSource to Ensuring[RefFlatSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. def ensuring(cond: (RefFlatSource) ⇒ Boolean): RefFlatSource
    Implicit
    This member is added by an implicit conversion from RefFlatSource to Ensuring[RefFlatSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: Boolean, msg: ⇒ Any): RefFlatSource
    Implicit
    This member is added by an implicit conversion from RefFlatSource to Ensuring[RefFlatSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. def ensuring(cond: Boolean): RefFlatSource
    Implicit
    This member is added by an implicit conversion from RefFlatSource to Ensuring[RefFlatSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  34. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  35. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  36. def exists(p: (Gene) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  37. def filter(p: (Gene) ⇒ Boolean): Iterable[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  38. def filterNot(p: (Gene) ⇒ Boolean): Iterable[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  39. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  40. def find(p: (Gene) ⇒ Boolean): Option[Gene]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  41. def flatMap[B, That](f: (Gene) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  42. def flatten[B](implicit asTraversable: (Gene) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    GenericTraversableTemplate
  43. def fold[A1 >: Gene](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  44. def foldLeft[B](z: B)(op: (B, Gene) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  45. def foldRight[B](z: B)(op: (Gene, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  46. def forall(p: (Gene) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  47. def foreach[U](f: (Gene) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  48. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from RefFlatSource to StringFormat[RefFlatSource] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  49. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  50. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  51. def groupBy[K](f: (Gene) ⇒ K): Map[K, Iterable[Gene]]
    Definition Classes
    TraversableLike → GenTraversableLike
  52. def grouped(size: Int): Iterator[Iterable[Gene]]
    Definition Classes
    IterableLike
  53. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  54. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  55. def head: Gene
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  56. def headOption: Option[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  57. def init: Iterable[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  58. def inits: Iterator[Iterable[Gene]]
    Definition Classes
    TraversableLike
  59. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  60. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  61. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  62. def iterator: Iterator[Gene]
    Definition Classes
    RefFlatSource → IterableLike → GenIterableLike
  63. def last: Gene
    Definition Classes
    TraversableLike → GenTraversableLike
  64. def lastOption: Option[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  65. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  66. def map[B, That](f: (Gene) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  67. def max[B >: Gene](implicit cmp: Ordering[B]): Gene
    Definition Classes
    TraversableOnce → GenTraversableOnce
  68. def maxBy[B](f: (Gene) ⇒ B)(implicit cmp: Ordering[B]): Gene
    Definition Classes
    TraversableOnce → GenTraversableOnce
  69. def min[B >: Gene](implicit cmp: Ordering[B]): Gene
    Definition Classes
    TraversableOnce → GenTraversableOnce
  70. def minBy[B](f: (Gene) ⇒ B)(implicit cmp: Ordering[B]): Gene
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  73. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  75. def newBuilder: Builder[Gene, Iterable[Gene]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  76. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  77. final def notify(): Unit
    Definition Classes
    AnyRef
  78. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  79. def par: ParIterable[Gene]
    Definition Classes
    Parallelizable
  80. def parCombiner: Combiner[Gene, ParIterable[Gene]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  81. def partition(p: (Gene) ⇒ Boolean): (Iterable[Gene], Iterable[Gene])
    Definition Classes
    TraversableLike → GenTraversableLike
  82. def product[B >: Gene](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  83. def reduce[A1 >: Gene](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def reduceLeft[B >: Gene](op: (B, Gene) ⇒ B): B
    Definition Classes
    TraversableOnce
  85. def reduceLeftOption[B >: Gene](op: (B, Gene) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. def reduceOption[A1 >: Gene](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. def reduceRight[B >: Gene](op: (Gene, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  88. def reduceRightOption[B >: Gene](op: (Gene, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. def repr: Iterable[Gene]
    Definition Classes
    TraversableLike → GenTraversableLike
  90. def reversed: List[Gene]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  91. def sameElements[B >: Gene](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  92. def scan[B >: Gene, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  93. def scanLeft[B, That](z: B)(op: (B, Gene) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Gene], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  94. def scanRight[B, That](z: B)(op: (Gene, B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Gene], 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.

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

  129. def unzip[A1, A2](implicit asPair: (Gene) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
    GenericTraversableTemplate
  130. def unzip3[A1, A2, A3](implicit asTriple: (Gene) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
    GenericTraversableTemplate
  131. def view(from: Int, until: Int): IterableView[Gene, Iterable[Gene]]
    Definition Classes
    IterableLike → TraversableLike
  132. def view: IterableView[Gene, Iterable[Gene]]
    Definition Classes
    IterableLike → TraversableLike
  133. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  134. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  135. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  136. def withFilter(p: (Gene) ⇒ Boolean): FilterMonadic[Gene, Iterable[Gene]]
    Definition Classes
    TraversableLike → FilterMonadic
  137. def zip[A1 >: Gene, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[Gene], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  138. def zipAll[B, A1 >: Gene, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[Gene], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  139. def zipWithIndex[A1 >: Gene, That](implicit bf: CanBuildFrom[Iterable[Gene], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  140. def →[B](y: B): (RefFlatSource, B)
    Implicit
    This member is added by an implicit conversion from RefFlatSource to ArrowAssoc[RefFlatSource] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: (Gene) ⇒ Boolean): TraversableOnce[Gene]
    Implicit
    This member is added by an implicit conversion from RefFlatSource to MonadOps[Gene] 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:
    (refFlatSource: MonadOps[Gene]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: (Gene) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from RefFlatSource to MonadOps[Gene] 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:
    (refFlatSource: MonadOps[Gene]).flatMap(f)
    Definition Classes
    MonadOps
  3. def flatten: Iterator[Transcript]
    Implicit
    This member is added by an implicit conversion from RefFlatSource to FlattenOps[Transcript] performed by method flattenTraversableOnce 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:
    (refFlatSource: FlattenOps[Transcript]).flatten
    Definition Classes
    FlattenOps
  4. def map[B](f: (Gene) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from RefFlatSource to MonadOps[Gene] 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:
    (refFlatSource: MonadOps[Gene]).map(f)
    Definition Classes
    MonadOps
  5. def withFilter(p: (Gene) ⇒ Boolean): Iterator[Gene]
    Implicit
    This member is added by an implicit conversion from RefFlatSource to MonadOps[Gene] 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:
    (refFlatSource: MonadOps[Gene]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from LazyLogging

Inherited from Closeable

Inherited from AutoCloseable

Inherited from Iterable[Gene]

Inherited from IterableLike[Gene, Iterable[Gene]]

Inherited from Equals

Inherited from GenIterable[Gene]

Inherited from GenIterableLike[Gene, Iterable[Gene]]

Inherited from Traversable[Gene]

Inherited from GenTraversable[Gene]

Inherited from GenericTraversableTemplate[Gene, Iterable]

Inherited from TraversableLike[Gene, Iterable[Gene]]

Inherited from GenTraversableLike[Gene, Iterable[Gene]]

Inherited from Parallelizable[Gene, ParIterable[Gene]]

Inherited from TraversableOnce[Gene]

Inherited from GenTraversableOnce[Gene]

Inherited from FilterMonadic[Gene, Iterable[Gene]]

Inherited from HasNewBuilder[Gene, Iterable[com.fulcrumgenomics.util.GeneAnnotations.Gene] @scala.annotation.unchecked.uncheckedVariance]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from RefFlatSource to MonadOps[Gene]

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

Inherited by implicit conversion flattenTraversableOnce from RefFlatSource to FlattenOps[Transcript]

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

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

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

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

Inherited by implicit conversion alternateImplicit from RefFlatSource to ForceImplicitAmbiguity

Ungrouped