c

com.fulcrumgenomics.umi

ConsensusCallingIterator

class ConsensusCallingIterator extends Iterator[SamRecord]

An iterator that consumes from an incoming iterator of SAMRecords and generates consensus read SAMRecords using the supplied caller.

Linear Supertypes
Iterator[SamRecord], TraversableOnce[SamRecord], GenTraversableOnce[SamRecord], AnyRef, Any
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Inherited
  1. ConsensusCallingIterator
  2. Iterator
  3. TraversableOnce
  4. GenTraversableOnce
  5. AnyRef
  6. 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 ConsensusCallingIterator(sourceIterator: Iterator[SamRecord], caller: UmiConsensusCaller[_], progress: Option[ProgressLogger] = None)

    sourceIterator

    an iterator of SAMRecords

    caller

    the consensus caller to use to call consensus reads

    progress

    an optional progress logger to which to log progress in input reads

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 ConsensusCallingIterator to any2stringadd[ConsensusCallingIterator] 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): (ConsensusCallingIterator, B)
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to ArrowAssoc[ConsensusCallingIterator] 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: BufferedIterator[SamRecord]
    Definition Classes
    Iterator
  15. val caller: UmiConsensusCaller[_]
  16. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  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 drop(n: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  27. def dropWhile(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  28. def duplicate: (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  29. def ensuring(cond: (ConsensusCallingIterator) ⇒ Boolean, msg: ⇒ Any): ConsensusCallingIterator
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to Ensuring[ConsensusCallingIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  30. def ensuring(cond: (ConsensusCallingIterator) ⇒ Boolean): ConsensusCallingIterator
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to Ensuring[ConsensusCallingIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. def ensuring(cond: Boolean, msg: ⇒ Any): ConsensusCallingIterator
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to Ensuring[ConsensusCallingIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: Boolean): ConsensusCallingIterator
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to Ensuring[ConsensusCallingIterator] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  34. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  35. def exists(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  36. def filter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  37. def filterNot(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  38. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  39. def find(p: (SamRecord) ⇒ Boolean): Option[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  40. def flatMap[B](f: (SamRecord) ⇒ GenTraversableOnce[B]): Iterator[B]
    Definition Classes
    Iterator
  41. def fold[A1 >: SamRecord](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  42. def foldLeft[B](z: B)(op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  43. def foldRight[B](z: B)(op: (SamRecord, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  44. def forall(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  45. def foreach[U](f: (SamRecord) ⇒ U): Unit
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  46. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to StringFormat[ConsensusCallingIterator] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  47. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  48. def grouped[B >: SamRecord](size: Int): GroupedIterator[B]
    Definition Classes
    Iterator
  49. def hasDefiniteSize: Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  50. def hasNext(): Boolean

    True if there are more consensus reads, false otherwise.

    True if there are more consensus reads, false otherwise.

    Definition Classes
    ConsensusCallingIterator → Iterator
  51. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  52. def indexOf[B >: SamRecord](elem: B, from: Int): Int
    Definition Classes
    Iterator
  53. def indexOf[B >: SamRecord](elem: B): Int
    Definition Classes
    Iterator
  54. def indexWhere(p: (SamRecord) ⇒ Boolean, from: Int): Int
    Definition Classes
    Iterator
  55. def indexWhere(p: (SamRecord) ⇒ Boolean): Int
    Definition Classes
    Iterator
  56. def isEmpty: Boolean
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  57. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  58. def isTraversableAgain: Boolean
    Definition Classes
    Iterator → GenTraversableOnce
  59. def length: Int
    Definition Classes
    Iterator
  60. def map[B](f: (SamRecord) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  61. def max[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  62. def maxBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  63. def min[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  64. def minBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  65. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  66. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  67. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  68. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  69. def next(): SamRecord

    Returns the next consensus read.

    Returns the next consensus read.

    Definition Classes
    ConsensusCallingIterator → Iterator
  70. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. final def notify(): Unit
    Definition Classes
    AnyRef
  72. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  73. def padTo[A1 >: SamRecord](len: Int, elem: A1): Iterator[A1]
    Definition Classes
    Iterator
  74. def partition(p: (SamRecord) ⇒ Boolean): (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  75. def patch[B >: SamRecord](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]
    Definition Classes
    Iterator
  76. def product[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  77. val progress: Option[ProgressLogger]
  78. def reduce[A1 >: SamRecord](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  79. def reduceLeft[B >: SamRecord](op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce
  80. def reduceLeftOption[B >: SamRecord](op: (B, SamRecord) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  81. def reduceOption[A1 >: SamRecord](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  82. def reduceRight[B >: SamRecord](op: (SamRecord, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  83. def reduceRightOption[B >: SamRecord](op: (SamRecord, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def reversed: List[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  85. def sameElements(that: Iterator[_]): Boolean
    Definition Classes
    Iterator
  86. def scanLeft[B](z: B)(op: (B, SamRecord) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  87. def scanRight[B](z: B)(op: (SamRecord, B) ⇒ B): Iterator[B]
    Definition Classes
    Iterator
  88. def seq: Iterator[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  89. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  91. def slice(from: Int, until: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  92. def sliceIterator(from: Int, until: Int): Iterator[SamRecord]
    Attributes
    protected
    Definition Classes
    Iterator
  93. def sliding[B >: SamRecord](size: Int, step: Int): GroupedIterator[B]
    Definition Classes
    Iterator
  94. def span(p: (SamRecord) ⇒ Boolean): (Iterator[SamRecord], Iterator[SamRecord])
    Definition Classes
    Iterator
  95. def sum[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  96. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  97. def take(n: Int): Iterator[SamRecord]
    Definition Classes
    Iterator
  98. def takeWhile(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  99. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SamRecord, Col[SamRecord]]): Col[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  100. def toArray[B >: SamRecord](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def toBuffer[B >: SamRecord]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def toIndexedSeq: IndexedSeq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def toIterable: Iterable[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def toIterator: Iterator[SamRecord]
    Definition Classes
    Iterator → GenTraversableOnce
  105. def toList: List[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def toMap[T, U](implicit ev: <:<[SamRecord, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def toSeq: Seq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. def toSet[B >: SamRecord]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  109. def toStream: Stream[SamRecord]
    Definition Classes
    Iterator → GenTraversableOnce
  110. def toString(): String
    Definition Classes
    Iterator → AnyRef → Any
  111. def toTraversable: Traversable[SamRecord]
    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  112. def toVector: Vector[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  113. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  114. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  115. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  116. def withFilter(p: (SamRecord) ⇒ Boolean): Iterator[SamRecord]
    Definition Classes
    Iterator
  117. def zip[B](that: Iterator[B]): Iterator[(SamRecord, B)]
    Definition Classes
    Iterator
  118. def zipAll[B, A1 >: SamRecord, B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]
    Definition Classes
    Iterator
  119. def zipWithIndex: Iterator[(SamRecord, Int)]
    Definition Classes
    Iterator
  120. def →[B](y: B): (ConsensusCallingIterator, B)
    Implicit
    This member is added by an implicit conversion from ConsensusCallingIterator to ArrowAssoc[ConsensusCallingIterator] 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 ConsensusCallingIterator 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:
    (consensusCallingIterator: 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 ConsensusCallingIterator 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:
    (consensusCallingIterator: 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 ConsensusCallingIterator 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:
    (consensusCallingIterator: 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 ConsensusCallingIterator 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:
    (consensusCallingIterator: MonadOps[SamRecord]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from Iterator[SamRecord]

Inherited from TraversableOnce[SamRecord]

Inherited from GenTraversableOnce[SamRecord]

Inherited from AnyRef

Inherited from Any

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from ConsensusCallingIterator to ForceImplicitAmbiguity

Ungrouped