org.bdgenomics.adam.converters

VCFLineParser

class VCFLineParser extends Iterator[VCFLine]

VCFLineParser is a line-by-line (streaming) parser for VCF files, written specifically to support light-weight creation of FlatGenotype records from large (multi-Gb, gzipped) VCF files.

Linear Supertypes
Iterator[VCFLine], TraversableOnce[VCFLine], GenTraversableOnce[VCFLine], AnyRef, Any
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Inherited
  1. VCFLineParser
  2. Iterator
  3. TraversableOnce
  4. GenTraversableOnce
  5. AnyRef
  6. Any
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Visibility
  1. Public
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Instance Constructors

  1. new VCFLineParser(inputStream: InputStream, sampleSubset: Option[Set[String]] = scala.None)

    inputStream

    An input stream containing the VCF contents

    sampleSubset

    An (optional) set of Strings, containing only those samples that should be parsed from the file. If this parameter is non-None, then only those samples (column names) in the set will be contained in the VCFLine values produced by this parser.

Type Members

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

    Definition Classes
    Iterator

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. def ++[B >: VCFLine](that: ⇒ GenTraversableOnce[B]): Iterator[B]

    Definition Classes
    Iterator

  5. def /:[B](z: B)(op: (B, VCFLine) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  6. def :\[B](z: B)(op: (VCFLine, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  7. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    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, VCFLine) ⇒ B, combop: (B, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  13. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  14. def buffered: BufferedIterator[VCFLine]

    Definition Classes
    Iterator

  15. def clone(): AnyRef

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

  16. def close(): Unit

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

    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[VCFLine, B]): Option[B]

    Definition Classes
    TraversableOnce

  19. def contains(elem: Any): Boolean

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce

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

    Definition Classes
    Iterator

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

  26. def drop(n: Int): Iterator[VCFLine]

    Definition Classes
    Iterator

  27. def dropWhile(p: (VCFLine) ⇒ Boolean): Iterator[VCFLine]

    Definition Classes
    Iterator

  28. def duplicate: (Iterator[VCFLine], Iterator[VCFLine])

    Definition Classes
    Iterator

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

    Definition Classes
    AnyRef

  30. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  31. def exists(p: (VCFLine) ⇒ Boolean): Boolean

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  32. def filter(p: (VCFLine) ⇒ Boolean): Iterator[VCFLine]

    Definition Classes
    Iterator

  33. def filterNot(p: (VCFLine) ⇒ Boolean): Iterator[VCFLine]

    Definition Classes
    Iterator

  34. def finalize(): Unit

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

  35. def find(p: (VCFLine) ⇒ Boolean): Option[VCFLine]

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  36. def flatMap[B](f: (VCFLine) ⇒ GenTraversableOnce[B]): Iterator[B]

    Definition Classes
    Iterator

  37. def fold[A1 >: VCFLine](z: A1)(op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce

  38. def foldLeft[B](z: B)(op: (B, VCFLine) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  39. def foldRight[B](z: B)(op: (VCFLine, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  40. def forall(p: (VCFLine) ⇒ Boolean): Boolean

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  41. def foreach[U](f: (VCFLine) ⇒ U): Unit

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

    Definition Classes
    AnyRef → Any

  43. def grouped[B >: VCFLine](size: Int): GroupedIterator[B]

    Definition Classes
    Iterator

  44. def hasDefiniteSize: Boolean

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  45. def hasNext: Boolean

    Definition Classes
    VCFLineParser → Iterator

  46. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  47. def indexOf[B >: VCFLine](elem: B): Int

    Definition Classes
    Iterator

  48. def indexWhere(p: (VCFLine) ⇒ Boolean): Int

    Definition Classes
    Iterator

  49. def isEmpty: Boolean

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  50. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  51. def isTraversableAgain: Boolean

    Definition Classes
    Iterator → GenTraversableOnce

  52. def length: Int

    Definition Classes
    Iterator

  53. def map[B](f: (VCFLine) ⇒ B): Iterator[B]

    Definition Classes
    Iterator

  54. def max[B >: VCFLine](implicit cmp: Ordering[B]): VCFLine

    Definition Classes
    TraversableOnce → GenTraversableOnce

  55. def maxBy[B](f: (VCFLine) ⇒ B)(implicit cmp: Ordering[B]): VCFLine

    Definition Classes
    TraversableOnce → GenTraversableOnce

  56. def min[B >: VCFLine](implicit cmp: Ordering[B]): VCFLine

    Definition Classes
    TraversableOnce → GenTraversableOnce

  57. def minBy[B](f: (VCFLine) ⇒ B)(implicit cmp: Ordering[B]): VCFLine

    Definition Classes
    TraversableOnce → GenTraversableOnce

  58. def mkString: String

    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def mkString(sep: String): String

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    AnyRef

  62. def next(): VCFLine

    Definition Classes
    VCFLineParser → Iterator

  63. var nextLine: VCFLine

  64. def nonEmpty: Boolean

    Definition Classes
    TraversableOnce → GenTraversableOnce

  65. final def notify(): Unit

    Definition Classes
    AnyRef

  66. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  67. def padTo[A1 >: VCFLine](len: Int, elem: A1): Iterator[A1]

    Definition Classes
    Iterator

  68. def partition(p: (VCFLine) ⇒ Boolean): (Iterator[VCFLine], Iterator[VCFLine])

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

  70. def product[B >: VCFLine](implicit num: Numeric[B]): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  71. val reader: BufferedReader

  72. def reduce[A1 >: VCFLine](op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce

  73. def reduceLeft[B >: VCFLine](op: (B, VCFLine) ⇒ B): B

    Definition Classes
    TraversableOnce

  74. def reduceLeftOption[B >: VCFLine](op: (B, VCFLine) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  75. def reduceOption[A1 >: VCFLine](op: (A1, A1) ⇒ A1): Option[A1]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  76. def reduceRight[B >: VCFLine](op: (VCFLine, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  77. def reduceRightOption[B >: VCFLine](op: (VCFLine, B) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reversed: List[VCFLine]

    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

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

    Definition Classes
    Iterator

  80. var sampleIndices: Seq[Int]

  81. var samples: Array[String]

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

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

  84. def seq: Iterator[VCFLine]

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  85. def size: Int

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIndexedSeq: IndexedSeq[VCFLine]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIterable: Iterable[VCFLine]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterator: Iterator[VCFLine]

    Definition Classes
    Iterator → GenTraversableOnce

  99. def toList: List[VCFLine]

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toSeq: Seq[VCFLine]

    Definition Classes
    TraversableOnce → GenTraversableOnce

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

    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toStream: Stream[VCFLine]

    Definition Classes
    Iterator → GenTraversableOnce

  104. def toString(): String

    Definition Classes
    Iterator → AnyRef → Any

  105. def toTraversable: Traversable[VCFLine]

    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  106. def toVector: Vector[VCFLine]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  107. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  110. def withFilter(p: (VCFLine) ⇒ Boolean): Iterator[VCFLine]

    Definition Classes
    Iterator

  111. def zip[B](that: Iterator[B]): Iterator[(VCFLine, B)]

    Definition Classes
    Iterator

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

    Definition Classes
    Iterator

  113. def zipWithIndex: Iterator[(VCFLine, Int)]

    Definition Classes
    Iterator

Deprecated Value Members

  1. def /:\[A1 >: VCFLine](z: A1)(op: (A1, A1) ⇒ A1): A1

    Definition Classes
    GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.10.0) use fold instead

Inherited from Iterator[VCFLine]

Inherited from TraversableOnce[VCFLine]

Inherited from GenTraversableOnce[VCFLine]

Inherited from AnyRef

Inherited from Any

Ungrouped