org.bdgenomics.adam.util

# IntervalListReader

###
Related Doc: package util

#### 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
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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

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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