Class/Object

org.hammerlab.bam.iterator

PosStream

Related Docs: object PosStream | package iterator

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case class PosStream(uncompressedBytes: UncompressedBytes, header: Header) extends PosStreamI[UncompressedBytes] with Product with Serializable

Non-seekable PosStreamI

Linear Supertypes
Serializable, Serializable, Product, Equals, PosStreamI[UncompressedBytes], RecordIterator[Pos, UncompressedBytes], Closeable, AutoCloseable, SimpleIterator[Pos], BufferedIterator[Pos], Iterator[Pos], TraversableOnce[Pos], GenTraversableOnce[Pos], AnyRef, Any
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Inherited
  1. PosStream
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. PosStreamI
  7. RecordIterator
  8. Closeable
  9. AutoCloseable
  10. SimpleIterator
  11. BufferedIterator
  12. Iterator
  13. TraversableOnce
  14. GenTraversableOnce
  15. AnyRef
  16. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new PosStream(uncompressedBytes: UncompressedBytes, header: Header)

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Type Members

  1. class GroupedIterator[B >: A] extends AbstractIterator[Seq[B]] with Iterator[Seq[B]]

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    Definition Classes
    Iterator

Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. def ++[B >: Pos](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  4. def /:[B](z: B)(op: (B, Pos) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: (Pos, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  6. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  7. def _advance: Option[Pos]

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    Attributes
    protected
    Definition Classes
    PosStreamI → SimpleIterator

  8. def addString(b: StringBuilder): StringBuilder

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    Definition Classes
    TraversableOnce

  9. def addString(b: StringBuilder, sep: String): StringBuilder

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    Definition Classes
    TraversableOnce

  10. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

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    Definition Classes
    TraversableOnce

  11. def aggregate[B](z: ⇒ B)(seqop: (B, Pos) ⇒ B, combop: (B, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  12. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  13. def buffered: PosStream.this.type

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    Definition Classes
    BufferedIterator → Iterator

  14. def clear(): Unit

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    Definition Classes
    SimpleIterator

  15. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  16. def close(): Unit

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    Definition Classes
    RecordIterator → Closeable → AutoCloseable

  17. def collect[B](pf: PartialFunction[Pos, B]): Iterator[B]

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    Definition Classes
    Iterator
    Annotations
    @migration
    Migration

    (Changed in version 2.8.0) collect has changed. The previous behavior can be reproduced with toSeq.

  18. def collectFirst[B](pf: PartialFunction[Pos, B]): Option[B]

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    Definition Classes
    TraversableOnce

  19. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

  20. def copyToArray[B >: Pos](xs: Array[B], start: Int, len: Int): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  21. def copyToArray[B >: Pos](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  22. def copyToArray[B >: Pos](xs: Array[B], start: Int): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  23. def copyToBuffer[B >: Pos](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

  24. def corresponds[B](that: GenTraversableOnce[B])(p: (Pos, B) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator

  25. def count(p: (Pos) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  26. def curBlock: Option[Block]

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    Definition Classes
    RecordIterator

  27. def curPos: Option[Pos]

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    Definition Classes
    RecordIterator

  28. def done(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  29. def drop(n: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  30. def dropWhile(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  31. def duplicate: (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

  32. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  33. def exists(p: (Pos) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  34. def filter(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  35. def filterNot(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  36. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  37. def find(p: (Pos) ⇒ Boolean): Option[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  38. def flatMap[B](f: (Pos) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  39. def fold[A1 >: Pos](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  40. def foldLeft[B](z: B)(op: (B, Pos) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  41. def foldRight[B](z: B)(op: (Pos, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  42. def forall(p: (Pos) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  43. def foreach[U](f: (Pos) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  44. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  45. def grouped[B >: Pos](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  46. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  47. final def hasNext: Boolean

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    Definition Classes
    SimpleIterator → Iterator

  48. final def head: Pos

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    Definition Classes
    SimpleIterator → BufferedIterator

  49. val header: Header

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    Definition Classes
    PosStream → RecordIterator

  50. def indexOf[B >: Pos](elem: B): Int

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    Definition Classes
    Iterator

  51. def indexWhere(p: (Pos) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  52. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  53. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  54. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  55. def length: Int

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    Definition Classes
    Iterator

  56. def map[B](f: (Pos) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  57. def max[B >: Pos](implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  58. def maxBy[B](f: (Pos) ⇒ B)(implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def min[B >: Pos](implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. def minBy[B](f: (Pos) ⇒ B)(implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  61. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  62. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  63. def mkString(start: String, sep: String, end: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  64. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  65. final def next(): Pos

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    Definition Classes
    SimpleIterator → Iterator

  66. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  67. final def notify(): Unit

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    Definition Classes
    AnyRef

  68. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  69. def padTo[A1 >: Pos](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

  70. def partition(p: (Pos) ⇒ Boolean): (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

  71. def patch[B >: Pos](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]

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    Definition Classes
    Iterator

  72. def postNext(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  73. def product[B >: Pos](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  74. def reduce[A1 >: Pos](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  75. def reduceLeft[B >: Pos](op: (B, Pos) ⇒ B): B

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    Definition Classes
    TraversableOnce

  76. def reduceLeftOption[B >: Pos](op: (B, Pos) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  77. def reduceOption[A1 >: Pos](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reduceRight[B >: Pos](op: (Pos, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  79. def reduceRightOption[B >: Pos](op: (Pos, B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  80. def reversed: List[Pos]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

  81. def sameElements(that: Iterator[_]): Boolean

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    Definition Classes
    Iterator

  82. def scanLeft[B](z: B)(op: (B, Pos) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  83. def scanRight[B](z: B)(op: (Pos, B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  84. def seq: Iterator[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  85. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  86. def slice(from: Int, until: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  87. def sliding[B >: Pos](size: Int, step: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  88. def span(p: (Pos) ⇒ Boolean): (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

  89. def sum[B >: Pos](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  90. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  91. def take(n: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  92. def takeWhile(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  93. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Pos, Col[Pos]]): Col[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  94. def toArray[B >: Pos](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toBuffer[B >: Pos]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIndexedSeq: IndexedSeq[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIterable: Iterable[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterator: Iterator[Pos]

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    Definition Classes
    Iterator → GenTraversableOnce

  99. def toList: List[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  100. def toMap[T, U](implicit ev: <:<[Pos, (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toSeq: Seq[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def toSet[B >: Pos]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toStream: Stream[Pos]

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    Definition Classes
    Iterator → GenTraversableOnce

  104. def toString(): String

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    Definition Classes
    SimpleIterator → Iterator → AnyRef → Any

  105. def toTraversable: Traversable[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  106. def toVector: Vector[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  107. val uncompressedByteChannel: ByteChannel

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    Definition Classes
    RecordIterator

  108. val uncompressedBytes: UncompressedBytes

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    Definition Classes
    PosStream → RecordIterator

  109. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  110. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  111. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  112. def withFilter(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  113. def zip[B](that: Iterator[B]): Iterator[(Pos, B)]

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    Definition Classes
    Iterator

  114. def zipAll[B, A1 >: Pos, B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]

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    Definition Classes
    Iterator

  115. def zipWithIndex: Iterator[(Pos, Int)]

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    Definition Classes
    Iterator

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from PosStreamI[UncompressedBytes]

Inherited from RecordIterator[Pos, UncompressedBytes]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from SimpleIterator[Pos]

Inherited from BufferedIterator[Pos]

Inherited from Iterator[Pos]

Inherited from TraversableOnce[Pos]

Inherited from GenTraversableOnce[Pos]

Inherited from AnyRef

Inherited from Any

Ungrouped