Class/Object

org.hammerlab.bam.iterator

RecordStream

Related Docs: object RecordStream | package iterator

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case class RecordStream[Stream <: UncompressedBytesI[_]](uncompressedBytes: Stream, header: Header) extends RecordStreamI[Stream] with Product with Serializable

Non-seekable RecordStreamI

Linear Supertypes
Serializable, Serializable, Product, Equals, RecordStreamI[Stream], RecordIterator[(Pos, SAMRecord), Stream], Closeable, AutoCloseable, SimpleIterator[(Pos, SAMRecord)], BufferedIterator[(Pos, SAMRecord)], Iterator[(Pos, SAMRecord)], TraversableOnce[(Pos, SAMRecord)], GenTraversableOnce[(Pos, SAMRecord)], AnyRef, Any
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Inherited
  1. RecordStream
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. RecordStreamI
  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 RecordStream(uncompressedBytes: Stream, 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, SAMRecord)](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Attributes
    protected
    Definition Classes
    RecordStreamI → 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, SAMRecord)) ⇒ 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. lazy val bamCodec: BAMRecordCodec

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    Definition Classes
    RecordStreamI

  14. def buffered: RecordStream.this.type

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    Definition Classes
    BufferedIterator → Iterator

  15. def clear(): Unit

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    Definition Classes
    SimpleIterator

  16. def clone(): AnyRef

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

  17. def close(): Unit

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    Definition Classes
    RecordIterator → Closeable → AutoCloseable

  18. def collect[B](pf: PartialFunction[(Pos, SAMRecord), 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.

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

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    Definition Classes
    TraversableOnce

  20. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  24. def copyToBuffer[B >: (Pos, SAMRecord)](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

  26. def count(p: ((Pos, SAMRecord)) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  27. def curBlock: Option[Block]

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    Definition Classes
    RecordIterator

  28. def curPos: Option[Pos]

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    Definition Classes
    RecordIterator

  29. def done(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  30. def drop(n: Int): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

  31. def dropWhile(p: ((Pos, SAMRecord)) ⇒ Boolean): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

  32. def duplicate: (Iterator[(Pos, SAMRecord)], Iterator[(Pos, SAMRecord)])

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    Definition Classes
    Iterator

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

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    Definition Classes
    AnyRef

  34. def exists(p: ((Pos, SAMRecord)) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  35. def filter(p: ((Pos, SAMRecord)) ⇒ Boolean): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

  36. def filterNot(p: ((Pos, SAMRecord)) ⇒ Boolean): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

  37. def finalize(): Unit

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

  38. def find(p: ((Pos, SAMRecord)) ⇒ Boolean): Option[(Pos, SAMRecord)]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  39. def flatMap[B](f: ((Pos, SAMRecord)) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  43. def forall(p: ((Pos, SAMRecord)) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  44. def foreach[U](f: ((Pos, SAMRecord)) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef → Any

  46. def grouped[B >: (Pos, SAMRecord)](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  47. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  48. final def hasNext: Boolean

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    Definition Classes
    SimpleIterator → Iterator

  49. final def head: (Pos, SAMRecord)

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    Definition Classes
    SimpleIterator → BufferedIterator

  50. val header: Header

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    Definition Classes
    RecordStream → RecordIterator

  51. def indexOf[B >: (Pos, SAMRecord)](elem: B): Int

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    Definition Classes
    Iterator

  52. def indexWhere(p: ((Pos, SAMRecord)) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  53. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  54. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  55. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  56. def length: Int

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    Definition Classes
    Iterator

  57. def map[B](f: ((Pos, SAMRecord)) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  58. def max[B >: (Pos, SAMRecord)](implicit cmp: Ordering[B]): (Pos, SAMRecord)

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def maxBy[B](f: ((Pos, SAMRecord)) ⇒ B)(implicit cmp: Ordering[B]): (Pos, SAMRecord)

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. def min[B >: (Pos, SAMRecord)](implicit cmp: Ordering[B]): (Pos, SAMRecord)

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  61. def minBy[B](f: ((Pos, SAMRecord)) ⇒ B)(implicit cmp: Ordering[B]): (Pos, SAMRecord)

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  62. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  63. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  66. final def next(): (Pos, SAMRecord)

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    Definition Classes
    SimpleIterator → Iterator

  67. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  68. final def notify(): Unit

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    Definition Classes
    AnyRef

  69. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  73. def postNext(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  74. def product[B >: (Pos, SAMRecord)](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  81. def reversed: List[(Pos, SAMRecord)]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  85. def seq: Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  86. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  90. def sum[B >: (Pos, SAMRecord)](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  92. def take(n: Int): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

  93. def takeWhile(p: ((Pos, SAMRecord)) ⇒ Boolean): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toArray[B >: (Pos, SAMRecord)](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toBuffer[B >: (Pos, SAMRecord)]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIndexedSeq: IndexedSeq[(Pos, SAMRecord)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterable: Iterable[(Pos, SAMRecord)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  99. def toIterator: Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator → GenTraversableOnce

  100. def toList: List[(Pos, SAMRecord)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def toSeq: Seq[(Pos, SAMRecord)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toSet[B >: (Pos, SAMRecord)]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  104. def toStream: Stream[(Pos, SAMRecord)]

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    Definition Classes
    Iterator → GenTraversableOnce

  105. def toString(): String

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    Definition Classes
    SimpleIterator → Iterator → AnyRef → Any

  106. def toTraversable: Traversable[(Pos, SAMRecord)]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  107. def toVector: Vector[(Pos, SAMRecord)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  108. val uncompressedByteChannel: ByteChannel

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    Definition Classes
    RecordIterator

  109. val uncompressedBytes: Stream

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    Definition Classes
    RecordStream → RecordIterator

  110. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  113. def withFilter(p: ((Pos, SAMRecord)) ⇒ Boolean): Iterator[(Pos, SAMRecord)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from RecordStreamI[Stream]

Inherited from RecordIterator[(Pos, SAMRecord), Stream]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from SimpleIterator[(Pos, SAMRecord)]

Inherited from BufferedIterator[(Pos, SAMRecord)]

Inherited from Iterator[(Pos, SAMRecord)]

Inherited from TraversableOnce[(Pos, SAMRecord)]

Inherited from GenTraversableOnce[(Pos, SAMRecord)]

Inherited from AnyRef

Inherited from Any

Ungrouped