final class SamIterator extends SelfClosingIterator[SamRecord] with HeaderHelper

An iterator over SamRecords that will automatically close the underlying iterator at the end of iteration, and provides access to the SAMFileHeader from the associated source.

Linear Supertypes
HeaderHelper, SelfClosingIterator[SamRecord], Closeable, AutoCloseable, BetterBufferedIterator[SamRecord], BufferedIterator[SamRecord], Iterator[SamRecord], TraversableOnce[SamRecord], GenTraversableOnce[SamRecord], HeadOption[SamRecord], AnyRef, Any
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  2. By Inheritance
Inherited
  1. SamIterator
  2. HeaderHelper
  3. SelfClosingIterator
  4. Closeable
  5. AutoCloseable
  6. BetterBufferedIterator
  7. BufferedIterator
  8. Iterator
  9. TraversableOnce
  10. GenTraversableOnce
  11. HeadOption
  12. AnyRef
  13. Any
Implicitly
  1. by MonadOps
  2. by any2stringadd
  3. by StringFormat
  4. by Ensuring
  5. by ArrowAssoc
  6. by alternateImplicit
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new SamIterator(header: SAMFileHeader, underlying: SAMRecordIterator)

Type Members

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

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from SamIterator to any2stringadd[SamIterator] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: SamRecord](that: ⇒ GenTraversableOnce[B]): Iterator[B]
    Definition Classes
    Iterator
  5. def ->[B](y: B): (SamIterator, B)
    Implicit
    This member is added by an implicit conversion from SamIterator to ArrowAssoc[SamIterator] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  6. def /:[B](z: B)(op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  7. def :\[B](z: B)(op: (SamRecord, 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, SamRecord) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  13. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  14. def buffered: SamIterator.this.type
    Definition Classes
    BufferedIterator → Iterator
  15. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  16. def close(): Unit
    Definition Classes
    SelfClosingIterator → Closeable → AutoCloseable
  17. def collect[B](pf: PartialFunction[SamRecord, 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[SamRecord, B]): Option[B]
    Definition Classes
    TraversableOnce
  19. def contains(elem: Any): Boolean
    Definition Classes
    Iterator
  20. def copyToArray[B >: SamRecord](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  21. def copyToArray[B >: SamRecord](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  22. def copyToArray[B >: SamRecord](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  23. def copyToBuffer[B >: SamRecord](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  24. def corresponds[B](that: GenTraversableOnce[B])(p: (SamRecord, B) ⇒ Boolean): Boolean
    Definition Classes
    Iterator
  25. def count(p: (SamRecord) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  26. def dict: SAMSequenceDictionary

    The sequence dictionary.

    The sequence dictionary.

    Definition Classes
    HeaderHelper
  27. def drop(n: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  28. def dropWhile(p: (SamRecord) ⇒ Boolean): SamIterator.this.type
    Definition Classes
    BetterBufferedIterator → Iterator
  29. def duplicate: (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  30. def ensuring(cond: (SamIterator) ⇒ Boolean, msg: ⇒ Any): SamIterator
    Implicit
    This member is added by an implicit conversion from SamIterator to Ensuring[SamIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. def ensuring(cond: (SamIterator) ⇒ Boolean): SamIterator
    Implicit
    This member is added by an implicit conversion from SamIterator to Ensuring[SamIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: Boolean, msg: ⇒ Any): SamIterator
    Implicit
    This member is added by an implicit conversion from SamIterator to Ensuring[SamIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. def ensuring(cond: Boolean): SamIterator
    Implicit
    This member is added by an implicit conversion from SamIterator to Ensuring[SamIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  34. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  35. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  36. def exists(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  37. def filter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  38. def filterNot(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  39. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  40. def find(p: (SamRecord) ⇒ Boolean): Option[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  41. def flatMap[B](f: (SamRecord) ⇒ GenTraversableOnce[B]): Iterator[B]
    Definition Classes
    Iterator
  42. def fold[A1 >: SamRecord](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  43. def foldLeft[B](z: B)(op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  44. def foldRight[B](z: B)(op: (SamRecord, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  45. def forall(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  46. def foreach[U](f: (SamRecord) ⇒ U): Unit
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  47. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SamIterator to StringFormat[SamIterator] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  48. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  49. def grouped[B >: SamRecord](size: Int): GroupedIterator[B]
    Definition Classes
    Iterator
  50. def hasDefiniteSize: Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  51. def hasNext: Boolean
    Definition Classes
    SelfClosingIterator → BetterBufferedIterator → Iterator
  52. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  53. def head: SamRecord
    Definition Classes
    BetterBufferedIterator → BufferedIterator
  54. def headOption: Option[SamRecord]
    Definition Classes
    BetterBufferedIterator → BufferedIterator → HeadOption
  55. val header: SAMFileHeader
    Definition Classes
    SamIterator → HeaderHelper
  56. def indexOf[B >: SamRecord](elem: B, from: Int): Int
    Definition Classes
    Iterator
  57. def indexOf[B >: SamRecord](elem: B): Int
    Definition Classes
    Iterator
  58. def indexWhere(p: (SamRecord) ⇒ Boolean, from: Int): Int
    Definition Classes
    Iterator
  59. def indexWhere(p: (SamRecord) ⇒ Boolean): Int
    Definition Classes
    Iterator
  60. def isEmpty: Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  61. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  62. def isTraversableAgain: Boolean
    Definition Classes
    Iterator → GenTraversableOnce
  63. def length: Int
    Definition Classes
    Iterator
  64. def map[B](f: (SamRecord) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  65. def max[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  66. def maxBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  67. def min[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  68. def minBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  69. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  70. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  73. def next(): SamRecord
    Definition Classes
    SelfClosingIterator → BetterBufferedIterator → Iterator
  74. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  75. final def notify(): Unit
    Definition Classes
    AnyRef
  76. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  77. def padTo[A1 >: SamRecord](len: Int, elem: A1): Iterator[A1]
    Definition Classes
    Iterator
  78. def partition(p: (SamRecord) ⇒ Boolean): (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  79. def patch[B >: SamRecord](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]
    Definition Classes
    Iterator
  80. def product[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  81. def programGroups: Seq[SAMProgramRecord]

    The list of program groups from the associated header.

    The list of program groups from the associated header.

    Definition Classes
    HeaderHelper
  82. def readGroups: Seq[SAMReadGroupRecord]

    The list of read groups from the associated header.

    The list of read groups from the associated header.

    Definition Classes
    HeaderHelper
  83. def reduce[A1 >: SamRecord](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def reduceLeft[B >: SamRecord](op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce
  85. def reduceLeftOption[B >: SamRecord](op: (B, SamRecord) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. def reduceOption[A1 >: SamRecord](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. def reduceRight[B >: SamRecord](op: (SamRecord, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  88. def reduceRightOption[B >: SamRecord](op: (SamRecord, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. def reversed: List[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  90. def sameElements(that: Iterator[_]): Boolean
    Definition Classes
    Iterator
  91. def scanLeft[B](z: B)(op: (B, SamRecord) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  92. def scanRight[B](z: B)(op: (SamRecord, B) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  93. def seq: Iterator[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  94. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  95. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  96. def slice(from: Int, until: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  97. def sliceIterator(from: Int, until: Int): Iterator[SamRecord]
    Attributes
    protected
    Definition Classes
    Iterator
  98. def sliding[B >: SamRecord](size: Int, step: Int): GroupedIterator[B]
    Definition Classes
    Iterator
  99. def span(p: (SamRecord) ⇒ Boolean): (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  100. def sum[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  102. def take(n: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  103. def takeWhile(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    BetterBufferedIterator → Iterator
  104. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SamRecord, Col[SamRecord]]): Col[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def toArray[B >: SamRecord](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def toBuffer[B >: SamRecord]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def toIndexedSeq: IndexedSeq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. def toIterable: Iterable[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  109. def toIterator: Iterator[SamRecord]
    Definition Classes
    Iterator → GenTraversableOnce
  110. def toList: List[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  111. def toMap[T, U](implicit ev: <:<[SamRecord, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  112. def toSeq: Seq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  113. def toSet[B >: SamRecord]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  114. def toStream: Stream[SamRecord]
    Definition Classes
    Iterator → GenTraversableOnce
  115. def toString(): String
    Definition Classes
    Iterator → AnyRef → Any
  116. def toTraversable: Traversable[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  117. def toVector: Vector[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  118. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  119. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  120. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  121. def withFilter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  122. def zip[B](that: Iterator[B]): Iterator[(SamRecord, B)]
    Definition Classes
    Iterator
  123. def zipAll[B, A1 >: SamRecord, B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]
    Definition Classes
    Iterator
  124. def zipWithIndex: Iterator[(SamRecord, Int)]
    Definition Classes
    Iterator
  125. def →[B](y: B): (SamIterator, B)
    Implicit
    This member is added by an implicit conversion from SamIterator to ArrowAssoc[SamIterator] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: (SamRecord) ⇒ Boolean): TraversableOnce[SamRecord]
    Implicit
    This member is added by an implicit conversion from SamIterator to MonadOps[SamRecord] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (samIterator: MonadOps[SamRecord]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: (SamRecord) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from SamIterator to MonadOps[SamRecord] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (samIterator: MonadOps[SamRecord]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: (SamRecord) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from SamIterator to MonadOps[SamRecord] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (samIterator: MonadOps[SamRecord]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Implicit
    This member is added by an implicit conversion from SamIterator to MonadOps[SamRecord] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (samIterator: MonadOps[SamRecord]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from HeaderHelper

Inherited from SelfClosingIterator[SamRecord]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from BetterBufferedIterator[SamRecord]

Inherited from BufferedIterator[SamRecord]

Inherited from Iterator[SamRecord]

Inherited from TraversableOnce[SamRecord]

Inherited from GenTraversableOnce[SamRecord]

Inherited from HeadOption[SamRecord]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from SamIterator to MonadOps[SamRecord]

Inherited by implicit conversion any2stringadd from SamIterator to any2stringadd[SamIterator]

Inherited by implicit conversion StringFormat from SamIterator to StringFormat[SamIterator]

Inherited by implicit conversion Ensuring from SamIterator to Ensuring[SamIterator]

Inherited by implicit conversion ArrowAssoc from SamIterator to ArrowAssoc[SamIterator]

Inherited by implicit conversion alternateImplicit from SamIterator to ForceImplicitAmbiguity

Ungrouped