class ReadStructure extends Seq[ReadSegment]

Describes the structure of a give read. A read contains one or more read segments. A read segment describes a contiguous stretch of bases of the same type (ex. template bases) of some length and some offset from the start of the read.

Linear Supertypes
Seq[ReadSegment], Seq[ReadSegment], SeqLike[ReadSegment, Seq[ReadSegment]], GenSeq[ReadSegment], GenSeqLike[ReadSegment, Seq[ReadSegment]], PartialFunction[Int, ReadSegment], (Int) ⇒ ReadSegment, Iterable[ReadSegment], Iterable[ReadSegment], IterableLike[ReadSegment, Seq[ReadSegment]], Equals, GenIterable[ReadSegment], GenIterableLike[ReadSegment, Seq[ReadSegment]], Traversable[ReadSegment], Immutable, Traversable[ReadSegment], GenTraversable[ReadSegment], GenericTraversableTemplate[ReadSegment, Seq], TraversableLike[ReadSegment, Seq[ReadSegment]], GenTraversableLike[ReadSegment, Seq[ReadSegment]], Parallelizable[ReadSegment, ParSeq[ReadSegment]], TraversableOnce[ReadSegment], GenTraversableOnce[ReadSegment], FilterMonadic[ReadSegment, Seq[ReadSegment]], HasNewBuilder[ReadSegment, scala.collection.immutable.Seq[com.fulcrumgenomics.util.ReadSegment] @scala.annotation.unchecked.uncheckedVariance], AnyRef, Any
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Inherited
  1. ReadStructure
  2. Seq
  3. Seq
  4. SeqLike
  5. GenSeq
  6. GenSeqLike
  7. PartialFunction
  8. Function1
  9. Iterable
  10. Iterable
  11. IterableLike
  12. Equals
  13. GenIterable
  14. GenIterableLike
  15. Traversable
  16. Immutable
  17. Traversable
  18. GenTraversable
  19. GenericTraversableTemplate
  20. TraversableLike
  21. GenTraversableLike
  22. Parallelizable
  23. TraversableOnce
  24. GenTraversableOnce
  25. FilterMonadic
  26. HasNewBuilder
  27. AnyRef
  28. Any
Implicitly
  1. by CollectionsHaveToParArray
  2. by MonadOps
  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 ReadStructure(readStructure: String)

    Creates a read structure from a string representation (ex.

    Creates a read structure from a string representation (ex. 8M150T8B).

  2. new ReadStructure(segs: Seq[ReadSegment], resetOffsets: Boolean = false)

    segs

    the segments composing this read structure.

    resetOffsets

    true if we are to update the offsets of each segment to be relative to each other, false otherwise. This may be useful to perform when segments are extracted from another read structure. New segment objects will be created in this case.

Type Members

  1. type Self = Seq[ReadSegment]
    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 ReadStructure to any2stringadd[ReadStructure] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: ReadSegment, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: ReadSegment, That](that: Traversable[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: ReadSegment, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike
  7. def +:[B >: ReadSegment, That](elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  8. def ->[B](y: B): (ReadStructure, B)
    Implicit
    This member is added by an implicit conversion from ReadStructure to ArrowAssoc[ReadStructure] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  9. def /:[B](z: B)(op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. def :+[B >: ReadSegment, That](elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  11. def :\[B](z: B)(op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  12. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  13. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  14. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  15. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  16. def aggregate[B](z: ⇒ B)(seqop: (B, ReadSegment) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  17. def andThen[C](k: (ReadSegment) ⇒ C): PartialFunction[Int, C]
    Definition Classes
    PartialFunction → Function1
  18. def apply(idx: Int): ReadSegment
    Definition Classes
    ReadStructure → SeqLike → GenSeqLike → Function1
  19. def applyOrElse[A1 <: Int, B1 >: ReadSegment](x: A1, default: (A1) ⇒ B1): B1
    Definition Classes
    PartialFunction
  20. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  21. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  22. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. def collect[B, That](pf: PartialFunction[ReadSegment, B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  24. def collectFirst[B](pf: PartialFunction[ReadSegment, B]): Option[B]
    Definition Classes
    TraversableOnce
  25. def combinations(n: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    SeqLike
  26. def companion: GenericCompanion[Seq]
    Definition Classes
    Seq → Seq → GenSeq → Iterable → Iterable → GenIterable → Traversable → Traversable → GenTraversable → GenericTraversableTemplate
  27. def compose[A](g: (A) ⇒ Int): (A) ⇒ ReadSegment
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  28. def contains[A1 >: ReadSegment](elem: A1): Boolean
    Definition Classes
    SeqLike
  29. def containsSlice[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike
  30. def copyToArray[B >: ReadSegment](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  31. def copyToArray[B >: ReadSegment](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  32. def copyToArray[B >: ReadSegment](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  33. def copyToBuffer[B >: ReadSegment](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  34. def corresponds[B](that: GenSeq[B])(p: (ReadSegment, B) ⇒ Boolean): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  35. def count(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def diff[B >: ReadSegment](that: GenSeq[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  37. def distinct: Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  38. def drop(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  39. def dropRight(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike
  40. def dropWhile(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  41. def endsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  42. def ensuring(cond: (ReadStructure) ⇒ Boolean, msg: ⇒ Any): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  43. def ensuring(cond: (ReadStructure) ⇒ Boolean): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  44. def ensuring(cond: Boolean, msg: ⇒ Any): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  45. def ensuring(cond: Boolean): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  46. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  47. def equals(that: Any): Boolean
    Definition Classes
    GenSeqLike → Equals → Any
  48. def exists(p: (ReadSegment) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  49. def filter(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  50. def filterNot(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  51. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  52. def find(p: (ReadSegment) ⇒ Boolean): Option[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  53. def flatMap[B, That](f: (ReadSegment) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  54. def flatten[B](implicit asTraversable: (ReadSegment) ⇒ GenTraversableOnce[B]): Seq[B]
    Definition Classes
    GenericTraversableTemplate
  55. def fold[A1 >: ReadSegment](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  56. def foldLeft[B](z: B)(op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  57. def foldRight[B](z: B)(op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  58. def forall(p: (ReadSegment) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  59. def foreach[U](f: (ReadSegment) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  60. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ReadStructure to StringFormat[ReadStructure] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  61. def genericBuilder[B]: Builder[B, Seq[B]]
    Definition Classes
    GenericTraversableTemplate
  62. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  63. def groupBy[K](f: (ReadSegment) ⇒ K): Map[K, Seq[ReadSegment]]
    Definition Classes
    TraversableLike → GenTraversableLike
  64. def grouped(size: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  65. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  66. def hashCode(): Int
    Definition Classes
    GenSeqLike → Any
  67. def head: ReadSegment
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  68. def headOption: Option[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  69. def indexOf[B >: ReadSegment](elem: B, from: Int): Int
    Definition Classes
    GenSeqLike
  70. def indexOf[B >: ReadSegment](elem: B): Int
    Definition Classes
    GenSeqLike
  71. def indexOfSlice[B >: ReadSegment](that: GenSeq[B], from: Int): Int
    Definition Classes
    SeqLike
  72. def indexOfSlice[B >: ReadSegment](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  73. def indexWhere(p: (ReadSegment) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  74. def indexWhere(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  75. def indices: Range
    Definition Classes
    SeqLike
  76. def init: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  77. def inits: Iterator[Seq[ReadSegment]]
    Definition Classes
    TraversableLike
  78. def intersect[B >: ReadSegment](that: GenSeq[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  79. def isDefinedAt(idx: Int): Boolean
    Definition Classes
    GenSeqLike
  80. def isEmpty: Boolean
    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  81. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  82. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  83. def iterator: Iterator[ReadSegment]
    Definition Classes
    ReadStructure → IterableLike → GenIterableLike
  84. def last: ReadSegment
    Definition Classes
    TraversableLike → GenTraversableLike
  85. def lastIndexOf[B >: ReadSegment](elem: B, end: Int): Int
    Definition Classes
    GenSeqLike
  86. def lastIndexOf[B >: ReadSegment](elem: B): Int
    Definition Classes
    GenSeqLike
  87. def lastIndexOfSlice[B >: ReadSegment](that: GenSeq[B], end: Int): Int
    Definition Classes
    SeqLike
  88. def lastIndexOfSlice[B >: ReadSegment](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  89. def lastIndexWhere(p: (ReadSegment) ⇒ Boolean, end: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  90. def lastIndexWhere(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  91. def lastOption: Option[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  92. def length: Int
    Definition Classes
    ReadStructure → SeqLike → GenSeqLike
  93. def lengthCompare(len: Int): Int
    Definition Classes
    SeqLike
  94. def lift: (Int) ⇒ Option[ReadSegment]
    Definition Classes
    PartialFunction
  95. def map[B, That](f: (ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  96. def max[B >: ReadSegment](implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  97. def maxBy[B](f: (ReadSegment) ⇒ B)(implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  98. def min[B >: ReadSegment](implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def minBy[B](f: (ReadSegment) ⇒ B)(implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  100. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def molecularBarcode: Seq[MolecularBarcode]
  104. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  105. def newBuilder: Builder[ReadSegment, Seq[ReadSegment]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  106. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. final def notify(): Unit
    Definition Classes
    AnyRef
  108. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  109. def orElse[A1 <: Int, B1 >: ReadSegment](that: PartialFunction[A1, B1]): PartialFunction[A1, B1]
    Definition Classes
    PartialFunction
  110. def padTo[B >: ReadSegment, That](len: Int, elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  111. def par: ParSeq[ReadSegment]
    Definition Classes
    Parallelizable
  112. def parCombiner: Combiner[ReadSegment, ParSeq[ReadSegment]]
    Attributes
    protected[this]
    Definition Classes
    Seq → SeqLike → Iterable → TraversableLike → Parallelizable
  113. def partition(p: (ReadSegment) ⇒ Boolean): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  114. def patch[B >: ReadSegment, That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  115. def permutations: Iterator[Seq[ReadSegment]]
    Definition Classes
    SeqLike
  116. def prefixLength(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  117. def product[B >: ReadSegment](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  118. def reduce[A1 >: ReadSegment](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  119. def reduceLeft[B >: ReadSegment](op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce
  120. def reduceLeftOption[B >: ReadSegment](op: (B, ReadSegment) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  121. def reduceOption[A1 >: ReadSegment](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  122. def reduceRight[B >: ReadSegment](op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  123. def reduceRightOption[B >: ReadSegment](op: (ReadSegment, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  124. def repr: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  125. def reverse: Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  126. def reverseIterator: Iterator[ReadSegment]
    Definition Classes
    SeqLike
  127. def reverseMap[B, That](f: (ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  128. def reversed: List[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  129. def runWith[U](action: (ReadSegment) ⇒ U): (Int) ⇒ Boolean
    Definition Classes
    PartialFunction
  130. def sameElements[B >: ReadSegment](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  131. def sampleBarcode: Seq[SampleBarcode]
  132. def scan[B >: ReadSegment, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  133. def scanLeft[B, That](z: B)(op: (B, ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  134. def scanRight[B, That](z: B)(op: (ReadSegment, B) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], 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.

  135. def segmentLength(p: (ReadSegment) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  136. def seq: Seq[ReadSegment]
    Definition Classes
    Seq → Seq → GenSeq → GenSeqLike → Iterable → Iterable → GenIterable → Traversable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  137. def size: Int
    Definition Classes
    SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce
  138. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  139. def skip: Seq[Skip]
  140. def slice(from: Int, until: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  141. def sliding(size: Int, step: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  142. def sliding(size: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  143. def sortBy[B](f: (ReadSegment) ⇒ B)(implicit ord: Ordering[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike
  144. def sortWith(lt: (ReadSegment, ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    SeqLike
  145. def sorted[B >: ReadSegment](implicit ord: Ordering[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike
  146. def span(p: (ReadSegment) ⇒ Boolean): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  147. def splitAt(n: Int): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  148. def startsWith[B](that: GenSeq[B], offset: Int): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  149. def startsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    GenSeqLike
  150. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  151. def structureRead(bases: String, strict: Boolean = true): Seq[SubRead]

    Splits the given bases into tuples with its associated read segment.

    Splits the given bases into tuples with its associated read segment. If strict is false then only return tuples for which we have bases in bases, otherwise throw an exception.

  152. def structureReadWithQualities(bases: String, qualities: String, strict: Boolean = true): Seq[SubRead]

    Splits the given bases and qualities into triples with its associated read segment.

    Splits the given bases and qualities into triples with its associated read segment. If strict is false then only return tuples for which we have bases in bases, otherwise throw an exception.

  153. def sum[B >: ReadSegment](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  154. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  155. def tail: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  156. def tails: Iterator[Seq[ReadSegment]]
    Definition Classes
    TraversableLike
  157. def take(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  158. def takeRight(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike
  159. def takeWhile(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  160. def template: Seq[Template]
  161. def thisCollection: Seq[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  162. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, ReadSegment, Col[ReadSegment]]): Col[ReadSegment]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  163. def toArray[B >: ReadSegment](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  164. def toBuffer[B >: ReadSegment]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  165. def toCollection(repr: Seq[ReadSegment]): Seq[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  166. def toIndexedSeq: IndexedSeq[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  167. def toIterable: Iterable[ReadSegment]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  168. def toIterator: Iterator[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  169. def toList: List[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  170. def toMap[T, U](implicit ev: <:<[ReadSegment, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  171. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from ReadStructure to CollectionsHaveToParArray[ReadStructure, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (ReadStructure) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
    CollectionsHaveToParArray
  172. def toSeq: Seq[ReadSegment]
    Definition Classes
    Seq → SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce
  173. def toSet[B >: ReadSegment]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  174. def toStream: Stream[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  175. def toString(): String
    Definition Classes
    ReadStructure → SeqLike → Function1 → TraversableLike → AnyRef → Any
  176. def toTraversable: Traversable[ReadSegment]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  177. def toVector: Vector[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  178. lazy val totalBases: Int
  179. def transpose[B](implicit asTraversable: (ReadSegment) ⇒ GenTraversableOnce[B]): Seq[Seq[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  180. def union[B >: ReadSegment, That](that: GenSeq[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  181. def unzip[A1, A2](implicit asPair: (ReadSegment) ⇒ (A1, A2)): (Seq[A1], Seq[A2])
    Definition Classes
    GenericTraversableTemplate
  182. def unzip3[A1, A2, A3](implicit asTriple: (ReadSegment) ⇒ (A1, A2, A3)): (Seq[A1], Seq[A2], Seq[A3])
    Definition Classes
    GenericTraversableTemplate
  183. def updated[B >: ReadSegment, That](index: Int, elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  184. def view(from: Int, until: Int): SeqView[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  185. def view: SeqView[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  186. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  187. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  188. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  189. def withFilter(p: (ReadSegment) ⇒ Boolean): FilterMonadic[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    TraversableLike → FilterMonadic
  190. def zip[A1 >: ReadSegment, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  191. def zipAll[B, A1 >: ReadSegment, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  192. def zipWithIndex[A1 >: ReadSegment, That](implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  193. def →[B](y: B): (ReadStructure, B)
    Implicit
    This member is added by an implicit conversion from ReadStructure to ArrowAssoc[ReadStructure] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

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

Inherited from Seq[ReadSegment]

Inherited from Seq[ReadSegment]

Inherited from SeqLike[ReadSegment, Seq[ReadSegment]]

Inherited from GenSeq[ReadSegment]

Inherited from GenSeqLike[ReadSegment, Seq[ReadSegment]]

Inherited from PartialFunction[Int, ReadSegment]

Inherited from (Int) ⇒ ReadSegment

Inherited from Iterable[ReadSegment]

Inherited from Iterable[ReadSegment]

Inherited from IterableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Equals

Inherited from GenIterable[ReadSegment]

Inherited from GenIterableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Traversable[ReadSegment]

Inherited from Immutable

Inherited from Traversable[ReadSegment]

Inherited from GenTraversable[ReadSegment]

Inherited from GenericTraversableTemplate[ReadSegment, Seq]

Inherited from TraversableLike[ReadSegment, Seq[ReadSegment]]

Inherited from GenTraversableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Parallelizable[ReadSegment, ParSeq[ReadSegment]]

Inherited from TraversableOnce[ReadSegment]

Inherited from GenTraversableOnce[ReadSegment]

Inherited from FilterMonadic[ReadSegment, Seq[ReadSegment]]

Inherited from HasNewBuilder[ReadSegment, scala.collection.immutable.Seq[com.fulcrumgenomics.util.ReadSegment] @scala.annotation.unchecked.uncheckedVariance]

Inherited from AnyRef

Inherited from Any

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

Inherited by implicit conversion MonadOps from ReadStructure to MonadOps[ReadSegment]

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

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

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

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

Inherited by implicit conversion alternateImplicit from ReadStructure to ForceImplicitAmbiguity

Ungrouped