Packages

abstract class KmerTable extends IndexedSeq[Array[Long]]

A k-mer table is a collection of k-mers, stored in column-major format. The first k-mer is stored in kmers(0)(0), kmers(1)(0), ... kmers(n)(0); the second in kmers(0)(1), kmers(1)(1)... kmers(n)(1) and so on. This layout enables fast radix sort. The KmerTable is optionally sorted by construction (by KmerTableBuilder). Each k-mer may contain additional annotation data ("tags") in longs following the sequence data itself.

Linear Supertypes
IndexedSeq[Array[Long]], IndexedSeqLike[Array[Long], IndexedSeq[Array[Long]]], Seq[Array[Long]], SeqLike[Array[Long], IndexedSeq[Array[Long]]], GenSeq[Array[Long]], GenSeqLike[Array[Long], IndexedSeq[Array[Long]]], Iterable[Array[Long]], IterableLike[Array[Long], IndexedSeq[Array[Long]]], Equals, GenIterable[Array[Long]], GenIterableLike[Array[Long], IndexedSeq[Array[Long]]], Traversable[Array[Long]], GenTraversable[Array[Long]], GenericTraversableTemplate[Array[Long], IndexedSeq], TraversableLike[Array[Long], IndexedSeq[Array[Long]]], GenTraversableLike[Array[Long], IndexedSeq[Array[Long]]], Parallelizable[Array[Long], ParSeq[Array[Long]]], TraversableOnce[Array[Long]], GenTraversableOnce[Array[Long]], FilterMonadic[Array[Long], IndexedSeq[Array[Long]]], HasNewBuilder[Array[Long], IndexedSeq[Array[Long]] @scala.annotation.unchecked.uncheckedVariance], PartialFunction[Int, Array[Long]], (Int) ⇒ Array[Long], AnyRef, Any
Known Subclasses
KmerTable1, KmerTable2, KmerTable3, KmerTable4, KmerTableN
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Inherited
  1. KmerTable
  2. IndexedSeq
  3. IndexedSeqLike
  4. Seq
  5. SeqLike
  6. GenSeq
  7. GenSeqLike
  8. Iterable
  9. IterableLike
  10. Equals
  11. GenIterable
  12. GenIterableLike
  13. Traversable
  14. GenTraversable
  15. GenericTraversableTemplate
  16. TraversableLike
  17. GenTraversableLike
  18. Parallelizable
  19. TraversableOnce
  20. GenTraversableOnce
  21. FilterMonadic
  22. HasNewBuilder
  23. PartialFunction
  24. Function1
  25. AnyRef
  26. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new KmerTable(kmers: Array[Array[Long]], width: Int, tagWidth: Int, k: Int)

    kmers

    k-mer data, column-major

    width

    number of columns (longs per row) in the table, including k-mer and tag data

    tagWidth

    number of additional columns on the right used for tag data

    k

    length of k-mers

Type Members

  1. class Elements extends AbstractIterator[A] with BufferedIterator[A] with Serializable
    Attributes
    protected
    Definition Classes
    IndexedSeqLike
    Annotations
    @SerialVersionUID()
  2. type Self = IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  3. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike

Abstract Value Members

  1. abstract def compareKmers(idx: Int, other: KmerTable, otherIdx: Int): Int

    Compare k-mer at position idx in this table with an equal length k-mer at position otherIdx in the other table.

    Compare k-mer at position idx in this table with an equal length k-mer at position otherIdx in the other table.

    idx

    Index in this table

    other

    Other table

    otherIdx

    Index in other table

    returns

    -1, 0, or 1 according to the Comparable contract (prior to, equal, or after)

  2. abstract def copyKmer(i: Int): Array[Long]

    Copy the k-mer at position i to a new long array.

  3. abstract def equalKmers(i: Int, kmer: Array[Long]): Boolean

    Test whether the k-mer at position i is equal to the given one.

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def ++[B >: Array[Long], That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  4. def ++:[B >: Array[Long], That](that: Traversable[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike
  5. def ++:[B >: Array[Long], That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike
  6. def +:[B >: Array[Long], That](elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  7. def :+[B >: Array[Long], That](elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  8. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  10. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  12. def aggregate[B](z: ⇒ B)(seqop: (B, Array[Long]) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  13. def andThen[C](k: (Array[Long]) ⇒ C): PartialFunction[Int, C]
    Definition Classes
    PartialFunction → Function1
  14. def apply(i: Int): Array[Long]

    K-mer only at position i

    K-mer only at position i

    Definition Classes
    KmerTable → SeqLike → GenSeqLike → Function1
  15. def applyOrElse[A1 <: Int, B1 >: Array[Long]](x: A1, default: (A1) ⇒ B1): B1
    Definition Classes
    PartialFunction
  16. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  17. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  18. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  19. def collect[B, That](pf: PartialFunction[Array[Long], B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  20. def collectFirst[B](pf: PartialFunction[Array[Long], B]): Option[B]
    Definition Classes
    TraversableOnce
  21. def combinations(n: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike
  22. def companion: GenericCompanion[IndexedSeq]
    Definition Classes
    IndexedSeq → Seq → GenSeq → Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  23. def compose[A](g: (A) ⇒ Int): (A) ⇒ Array[Long]
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  24. def contains[A1 >: Array[Long]](elem: A1): Boolean
    Definition Classes
    SeqLike
  25. def containsSlice[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike
  26. def copyKmerAndTags(i: Int): Array[Long]

    Copy k-mer and tags at position i to a new long array.

  27. def copyKmerAndTagsToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy k-mer and tag data from position i to a builder.

  28. def copyKmerOnlyToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy k-mer data only from position i to a builder.

  29. def copyTagsOnlyToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy tag data only from position i to a builder.

  30. def copyToArray[B >: Array[Long]](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  31. def copyToArray[B >: Array[Long]](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  32. def copyToArray[B >: Array[Long]](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  33. def copyToBuffer[B >: Array[Long]](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  34. def corresponds[B](that: GenSeq[B])(p: (Array[Long], B) ⇒ Boolean): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  35. def count(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def countedKmers: Iterator[(Array[Long], Abundance)]

    An iterator of distinct k-mers and their counts.

    An iterator of distinct k-mers and their counts. Requires that the KmerTable was sorted at construction time.

  37. def diff[B >: Array[Long]](that: GenSeq[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  38. def distinct: IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  39. def drop(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  40. def dropRight(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike
  41. def dropWhile(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  42. def endsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  43. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  44. def equals(that: Any): Boolean
    Definition Classes
    GenSeqLike → Equals → Any
  45. def exists(p: (Array[Long]) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  46. def filter(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  47. def filterNot(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  48. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  49. def find(p: (Array[Long]) ⇒ Boolean): Option[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  50. def flatMap[B, That](f: (Array[Long]) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  51. def flatten[B](implicit asTraversable: (Array[Long]) ⇒ GenTraversableOnce[B]): IndexedSeq[B]
    Definition Classes
    GenericTraversableTemplate
  52. def fold[A1 >: Array[Long]](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  53. def foldLeft[B](z: B)(op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  54. def foldRight[B](z: B)(op: (Array[Long], B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  55. def forall(p: (Array[Long]) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  56. def foreach[U](f: (Array[Long]) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  57. def genericBuilder[B]: Builder[B, IndexedSeq[B]]
    Definition Classes
    GenericTraversableTemplate
  58. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  59. def groupBy[K](f: (Array[Long]) ⇒ K): Map[K, IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike → GenTraversableLike
  60. def grouped(size: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  61. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  62. def hashCode(): Int
    Definition Classes
    IndexedSeqLike → GenSeqLike → Any
  63. def head: Array[Long]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  64. def headOption: Option[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  65. def indexIterator: Iterator[Int]
  66. def indexOf[B >: Array[Long]](elem: B, from: Int): Int
    Definition Classes
    GenSeqLike
  67. def indexOf[B >: Array[Long]](elem: B): Int
    Definition Classes
    GenSeqLike
  68. def indexOfSlice[B >: Array[Long]](that: GenSeq[B], from: Int): Int
    Definition Classes
    SeqLike
  69. def indexOfSlice[B >: Array[Long]](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  70. def indexWhere(p: (Array[Long]) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  71. def indexWhere(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  72. def indices: Range
    Definition Classes
    SeqLike
  73. def init: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  74. def inits: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike
  75. def intersect[B >: Array[Long]](that: GenSeq[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  76. def isDefinedAt(idx: Int): Boolean
    Definition Classes
    GenSeqLike
  77. def isEmpty: Boolean
    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  78. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  79. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  80. def iterator: Iterator[Array[Long]]

    Iterator with k-mer data only

    Iterator with k-mer data only

    Definition Classes
    KmerTable → IndexedSeqLike → IterableLike → GenIterableLike
  81. def iteratorWithTags: Iterator[Array[Long]]

    Iterator including both k-mer data and tag data

  82. val k: Int
  83. val kmerWidth: Int
  84. def kmerWithTags(i: Int): Array[Long]

    K-mer and tags at position i

  85. val kmers: Array[Array[Long]]
  86. def last: Array[Long]
    Definition Classes
    TraversableLike → GenTraversableLike
  87. def lastIndexOf[B >: Array[Long]](elem: B, end: Int): Int
    Definition Classes
    GenSeqLike
  88. def lastIndexOf[B >: Array[Long]](elem: B): Int
    Definition Classes
    GenSeqLike
  89. def lastIndexOfSlice[B >: Array[Long]](that: GenSeq[B], end: Int): Int
    Definition Classes
    SeqLike
  90. def lastIndexOfSlice[B >: Array[Long]](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  91. def lastIndexWhere(p: (Array[Long]) ⇒ Boolean, end: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  92. def lastIndexWhere(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  93. def lastOption: Option[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  94. def length: Int
    Definition Classes
    KmerTable → SeqLike → GenSeqLike
  95. def lengthCompare(len: Int): Int
    Definition Classes
    SeqLike
  96. def lift: (Int) ⇒ Option[Array[Long]]
    Definition Classes
    PartialFunction
  97. def map[B, That](f: (Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  98. def max[B >: Array[Long]](implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def maxBy[B](f: (Array[Long]) ⇒ B)(implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  100. def min[B >: Array[Long]](implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def minBy[B](f: (Array[Long]) ⇒ B)(implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  106. def newBuilder: Builder[Array[Long], IndexedSeq[Array[Long]]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  107. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  109. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  110. def orElse[A1 <: Int, B1 >: Array[Long]](that: PartialFunction[A1, B1]): PartialFunction[A1, B1]
    Definition Classes
    PartialFunction
  111. def padTo[B >: Array[Long], That](len: Int, elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  112. def par: ParSeq[Array[Long]]
    Definition Classes
    Parallelizable
  113. def parCombiner: Combiner[Array[Long], ParSeq[Array[Long]]]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → TraversableLike → Parallelizable
  114. def partition(p: (Array[Long]) ⇒ Boolean): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  115. def patch[B >: Array[Long], That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  116. def permutations: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike
  117. def prefixLength(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  118. def product[B >: Array[Long]](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  119. def reduce[A1 >: Array[Long]](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  120. def reduceLeft[B >: Array[Long]](op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce
  121. def reduceLeftOption[B >: Array[Long]](op: (B, Array[Long]) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  122. def reduceOption[A1 >: Array[Long]](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  123. def reduceRight[B >: Array[Long]](op: (Array[Long], B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  124. def reduceRightOption[B >: Array[Long]](op: (Array[Long], B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  125. def repr: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  126. def reverse: IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  127. def reverseIterator: Iterator[Array[Long]]
    Definition Classes
    SeqLike
  128. def reverseMap[B, That](f: (Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  129. def reversed: List[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  130. def runWith[U](action: (Array[Long]) ⇒ U): (Int) ⇒ Boolean
    Definition Classes
    PartialFunction
  131. def sameElements[B >: Array[Long]](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  132. def scan[B >: Array[Long], That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  133. def scanLeft[B, That](z: B)(op: (B, Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  134. def scanRight[B, That](z: B)(op: (Array[Long], B) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], 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: (Array[Long]) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  136. def seq: IndexedSeq[Array[Long]]
    Definition Classes
    IndexedSeq → IndexedSeqLike → Seq → GenSeq → GenSeqLike → Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  137. val size: Int
    Definition Classes
    KmerTable → SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce
  138. def sizeHintIfCheap: Int
    Attributes
    protected[collection]
    Definition Classes
    IndexedSeqLike → GenTraversableOnce
  139. def slice(from: Int, until: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  140. def sliding(size: Int, step: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  141. def sliding(size: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  142. def sortBy[B](f: (Array[Long]) ⇒ B)(implicit ord: Ordering[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  143. def sortWith(lt: (Array[Long], Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  144. def sorted[B >: Array[Long]](implicit ord: Ordering[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  145. def span(p: (Array[Long]) ⇒ Boolean): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  146. def splitAt(n: Int): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  147. def startsWith[B](that: GenSeq[B], offset: Int): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  148. def startsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    GenSeqLike
  149. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  150. def sum[B >: Array[Long]](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  151. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  152. val tagWidth: Int
  153. def tagsIterator: Iterator[Array[Long]]

    Iterator including only tags data

  154. def tagsOnly(i: Int): Array[Long]

    Tags only at position i

  155. def tail: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  156. def tails: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike
  157. def take(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  158. def takeRight(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike
  159. def takeWhile(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  160. def thisCollection: IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike
  161. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Array[Long], Col[Array[Long]]]): Col[Array[Long]]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  162. def toArray[B >: Array[Long]](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  163. def toBuffer[A1 >: Array[Long]]: Buffer[A1]
    Definition Classes
    IndexedSeqLike → TraversableOnce → GenTraversableOnce
  164. def toCollection(repr: IndexedSeq[Array[Long]]): IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike
  165. def toIndexedSeq: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  166. def toIterable: Iterable[Array[Long]]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  167. def toIterator: Iterator[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  168. def toList: List[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  169. def toMap[T, U](implicit ev: <:<[Array[Long], (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  170. def toSeq: Seq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce
  171. def toSet[B >: Array[Long]]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  172. def toStream: Stream[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  173. def toString(): String
    Definition Classes
    KmerTable → SeqLike → TraversableLike → Function1 → AnyRef → Any
  174. def toTraversable: Traversable[Array[Long]]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  175. def toVector: Vector[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  176. def transpose[B](implicit asTraversable: (Array[Long]) ⇒ GenTraversableOnce[B]): IndexedSeq[IndexedSeq[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  177. def union[B >: Array[Long], That](that: GenSeq[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  178. def unzip[A1, A2](implicit asPair: (Array[Long]) ⇒ (A1, A2)): (IndexedSeq[A1], IndexedSeq[A2])
    Definition Classes
    GenericTraversableTemplate
  179. def unzip3[A1, A2, A3](implicit asTriple: (Array[Long]) ⇒ (A1, A2, A3)): (IndexedSeq[A1], IndexedSeq[A2], IndexedSeq[A3])
    Definition Classes
    GenericTraversableTemplate
  180. def updated[B >: Array[Long], That](index: Int, elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  181. def view(from: Int, until: Int): SeqView[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  182. def view: SeqView[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  183. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  184. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  185. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  186. val width: Int
  187. def withFilter(p: (Array[Long]) ⇒ Boolean): FilterMonadic[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike → FilterMonadic
  188. def zip[A1 >: Array[Long], B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  189. def zipAll[B, A1 >: Array[Long], That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  190. def zipWithIndex[A1 >: Array[Long], That](implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike

Deprecated Value Members

  1. def /:[B](z: B)(op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldLeft instead of /:

  2. def :\[B](z: B)(op: (Array[Long], B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldRight instead of :\

Inherited from IndexedSeq[Array[Long]]

Inherited from IndexedSeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Seq[Array[Long]]

Inherited from SeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from GenSeq[Array[Long]]

Inherited from GenSeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Iterable[Array[Long]]

Inherited from IterableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Equals

Inherited from GenIterable[Array[Long]]

Inherited from GenIterableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Traversable[Array[Long]]

Inherited from GenTraversable[Array[Long]]

Inherited from GenericTraversableTemplate[Array[Long], IndexedSeq]

Inherited from TraversableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from GenTraversableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Parallelizable[Array[Long], ParSeq[Array[Long]]]

Inherited from TraversableOnce[Array[Long]]

Inherited from GenTraversableOnce[Array[Long]]

Inherited from FilterMonadic[Array[Long], IndexedSeq[Array[Long]]]

Inherited from HasNewBuilder[Array[Long], IndexedSeq[Array[Long]] @scala.annotation.unchecked.uncheckedVariance]

Inherited from PartialFunction[Int, Array[Long]]

Inherited from (Int) ⇒ Array[Long]

Inherited from AnyRef

Inherited from Any

Ungrouped