org.bdgenomics.adam.util

IntervalListReader

class IntervalListReader extends Traversable[(ReferenceRegion, String)]

Reads GATK-style interval list files e.g. example file taken from this page: http://www.broadinstitute.org/gatk/guide/article?id=1204

Linear Supertypes
Traversable[(ReferenceRegion, String)], GenTraversable[(ReferenceRegion, String)], GenericTraversableTemplate[(ReferenceRegion, String), Traversable], TraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], GenTraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], Parallelizable[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]], TraversableOnce[(ReferenceRegion, String)], GenTraversableOnce[(ReferenceRegion, String)], FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], HasNewBuilder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. IntervalListReader
  2. Traversable
  3. GenTraversable
  4. GenericTraversableTemplate
  5. TraversableLike
  6. GenTraversableLike
  7. Parallelizable
  8. TraversableOnce
  9. GenTraversableOnce
  10. FilterMonadic
  11. HasNewBuilder
  12. AnyRef
  13. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new IntervalListReader(file: File)

    file

    a File whose contents are a (line-based tab-separated) interval file in UTF-8 encoding

Type Members

  1. type Self = Traversable[(ReferenceRegion, String)]

    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 ++[B >: (ReferenceRegion, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike
  4. def ++:[B >: (ReferenceRegion, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike
  5. def ++:[B >: (ReferenceRegion, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike
  6. def /:[B](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  7. def :\[B](z: B)(op: ((ReferenceRegion, String), B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  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, (ReferenceRegion, String)) ⇒ B, combop: (B, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  13. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  14. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  15. def collect[B, That](pf: PartialFunction[(ReferenceRegion, String), B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike
  16. def collectFirst[B](pf: PartialFunction[(ReferenceRegion, String), B]): Option[B]

    Definition Classes
    TraversableOnce
  17. def companion: GenericCompanion[Traversable]

    Definition Classes
    Traversable → GenTraversable → GenericTraversableTemplate
  18. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B], start: Int, len: Int): Unit

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  19. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B]): Unit

    Definition Classes
    TraversableOnce → GenTraversableOnce
  20. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B], start: Int): Unit

    Definition Classes
    TraversableOnce → GenTraversableOnce
  21. def copyToBuffer[B >: (ReferenceRegion, String)](dest: Buffer[B]): Unit

    Definition Classes
    TraversableOnce
  22. def count(p: ((ReferenceRegion, String)) ⇒ Boolean): Int

    Definition Classes
    TraversableOnce → GenTraversableOnce
  23. def drop(n: Int): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  24. def dropWhile(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  25. val encoding: String

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

    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  28. def exists(p: ((ReferenceRegion, String)) ⇒ Boolean): Boolean

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  29. def filter(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  30. def filterNot(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  31. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def find(p: ((ReferenceRegion, String)) ⇒ Boolean): Option[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  33. def flatMap[B, That](f: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  34. def flatten[B](implicit asTraversable: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B]): Traversable[B]

    Definition Classes
    GenericTraversableTemplate
  35. def fold[A1 >: (ReferenceRegion, String)](z: A1)(op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def foldLeft[B](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  37. def foldRight[B](z: B)(op: ((ReferenceRegion, String), B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  38. def forall(p: ((ReferenceRegion, String)) ⇒ Boolean): Boolean

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  39. def foreach[U](f: ((ReferenceRegion, String)) ⇒ U): Unit

    Definition Classes
    IntervalListReader → GenericTraversableTemplate → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  40. def genericBuilder[B]: Builder[B, Traversable[B]]

    Definition Classes
    GenericTraversableTemplate
  41. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  42. def groupBy[K](f: ((ReferenceRegion, String)) ⇒ K): Map[K, Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike → GenTraversableLike
  43. def hasDefiniteSize: Boolean

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  44. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  45. def head: (ReferenceRegion, String)

    Definition Classes
    TraversableLike → GenTraversableLike
  46. def headOption: Option[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  47. def init: Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  48. def inits: Iterator[Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike
  49. def isEmpty: Boolean

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  50. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  51. final def isTraversableAgain: Boolean

    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  52. def last: (ReferenceRegion, String)

    Definition Classes
    TraversableLike → GenTraversableLike
  53. def lastOption: Option[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  54. def map[B, That](f: ((ReferenceRegion, String)) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  55. def max[B >: (ReferenceRegion, String)](implicit cmp: Ordering[B]): (ReferenceRegion, String)

    Definition Classes
    TraversableOnce → GenTraversableOnce
  56. def maxBy[B](f: ((ReferenceRegion, String)) ⇒ B)(implicit cmp: Ordering[B]): (ReferenceRegion, String)

    Definition Classes
    TraversableOnce → GenTraversableOnce
  57. def min[B >: (ReferenceRegion, String)](implicit cmp: Ordering[B]): (ReferenceRegion, String)

    Definition Classes
    TraversableOnce → GenTraversableOnce
  58. def minBy[B](f: ((ReferenceRegion, String)) ⇒ B)(implicit cmp: Ordering[B]): (ReferenceRegion, String)

    Definition Classes
    TraversableOnce → GenTraversableOnce
  59. def mkString: String

    Definition Classes
    TraversableOnce → GenTraversableOnce
  60. def mkString(sep: String): String

    Definition Classes
    TraversableOnce → GenTraversableOnce
  61. def mkString(start: String, sep: String, end: String): String

    Definition Classes
    TraversableOnce → GenTraversableOnce
  62. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  63. def newBuilder: Builder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  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 par: ParIterable[(ReferenceRegion, String)]

    Definition Classes
    Parallelizable
  68. def parCombiner: Combiner[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]]

    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  69. def partition(p: ((ReferenceRegion, String)) ⇒ Boolean): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

    Definition Classes
    TraversableLike → GenTraversableLike
  70. def product[B >: (ReferenceRegion, String)](implicit num: Numeric[B]): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def reduce[A1 >: (ReferenceRegion, String)](op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def reduceLeft[B >: (ReferenceRegion, String)](op: (B, (ReferenceRegion, String)) ⇒ B): B

    Definition Classes
    TraversableOnce
  73. def reduceLeftOption[B >: (ReferenceRegion, String)](op: (B, (ReferenceRegion, String)) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. def reduceOption[A1 >: (ReferenceRegion, String)](op: (A1, A1) ⇒ A1): Option[A1]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  75. def reduceRight[B >: (ReferenceRegion, String)](op: ((ReferenceRegion, String), B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  76. def reduceRightOption[B >: (ReferenceRegion, String)](op: ((ReferenceRegion, String), B) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  77. def repr: Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  78. def reversed: List[(ReferenceRegion, String)]

    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  79. def scan[B >: (ReferenceRegion, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike
  80. def scanLeft[B, That](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike
  81. def scanRight[B, That](z: B)(op: ((ReferenceRegion, String), B) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], 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.

  82. def seq: Traversable[(ReferenceRegion, String)]

    Definition Classes
    Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  83. lazy val sequenceDictionary: SequenceDictionary

    The interval list file contains a SAM-style sequence dictionary as a header -- this value holds that dictionary, reading it if necessary (if the file hasn't been opened before).

  84. def size: Int

    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def slice(from: Int, until: Int): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  86. def span(p: ((ReferenceRegion, String)) ⇒ Boolean): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

    Definition Classes
    TraversableLike → GenTraversableLike
  87. def splitAt(n: Int): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

    Definition Classes
    TraversableLike → GenTraversableLike
  88. def stringPrefix: String

    Definition Classes
    TraversableLike → GenTraversableLike
  89. def sum[B >: (ReferenceRegion, String)](implicit num: Numeric[B]): B

    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  91. def tail: Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  92. def tails: Iterator[Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike
  93. def take(n: Int): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  94. def takeWhile(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableLike
  95. def thisCollection: Traversable[(ReferenceRegion, String)]

    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  96. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (ReferenceRegion, String), Col[(ReferenceRegion, String)]]): Col[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  97. def toArray[B >: (ReferenceRegion, String)](implicit arg0: ClassTag[B]): Array[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  98. def toBuffer[B >: (ReferenceRegion, String)]: Buffer[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def toCollection(repr: Traversable[(ReferenceRegion, String)]): Traversable[(ReferenceRegion, String)]

    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  100. def toIndexedSeq: IndexedSeq[(ReferenceRegion, String)]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def toIterable: Iterable[(ReferenceRegion, String)]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def toIterator: Iterator[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableOnce
  103. def toList: List[(ReferenceRegion, String)]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def toMap[T, U](implicit ev: <:<[(ReferenceRegion, String), (T, U)]): Map[T, U]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def toSeq: Seq[(ReferenceRegion, String)]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def toSet[B >: (ReferenceRegion, String)]: Set[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def toStream: Stream[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → GenTraversableOnce
  108. def toString(): String

    Definition Classes
    TraversableLike → Any
  109. def toTraversable: Traversable[(ReferenceRegion, String)]

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  110. def toVector: Vector[(ReferenceRegion, String)]

    Definition Classes
    TraversableOnce → GenTraversableOnce
  111. def transpose[B](implicit asTraversable: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B]): Traversable[Traversable[B]]

    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  112. def unzip[A1, A2](implicit asPair: ((ReferenceRegion, String)) ⇒ (A1, A2)): (Traversable[A1], Traversable[A2])

    Definition Classes
    GenericTraversableTemplate
  113. def unzip3[A1, A2, A3](implicit asTriple: ((ReferenceRegion, String)) ⇒ (A1, A2, A3)): (Traversable[A1], Traversable[A2], Traversable[A3])

    Definition Classes
    GenericTraversableTemplate
  114. def view(from: Int, until: Int): TraversableView[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike
  115. def view: TraversableView[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike
  116. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  117. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  118. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  119. def withFilter(p: ((ReferenceRegion, String)) ⇒ Boolean): FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

    Definition Classes
    TraversableLike → FilterMonadic

Inherited from Traversable[(ReferenceRegion, String)]

Inherited from GenTraversable[(ReferenceRegion, String)]

Inherited from GenericTraversableTemplate[(ReferenceRegion, String), Traversable]

Inherited from TraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from GenTraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from Parallelizable[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]]

Inherited from TraversableOnce[(ReferenceRegion, String)]

Inherited from GenTraversableOnce[(ReferenceRegion, String)]

Inherited from FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from HasNewBuilder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from AnyRef

Inherited from Any

Ungrouped