class SamSource extends IterableView[SamRecord, SamSource] with HeaderHelper with Closeable

Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SamSource
  2. Closeable
  3. AutoCloseable
  4. HeaderHelper
  5. IterableView
  6. IterableViewLike
  7. TraversableView
  8. TraversableViewLike
  9. ViewMkString
  10. Iterable
  11. IterableLike
  12. Equals
  13. GenIterable
  14. GenIterableLike
  15. Traversable
  16. GenTraversable
  17. GenericTraversableTemplate
  18. TraversableLike
  19. GenTraversableLike
  20. Parallelizable
  21. TraversableOnce
  22. GenTraversableOnce
  23. FilterMonadic
  24. HasNewBuilder
  25. AnyRef
  26. Any
Implicitly
  1. by MonadOps
  2. by CollectionsHaveToParArray
  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
  7. by alternateImplicit
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Type Members

  1. trait Appended[B >: A] extends scala.collection.IterableViewLike.Appended[B] with Transformed[B]
    Definition Classes
    IterableViewLike
  2. trait DroppedWhile extends scala.collection.IterableViewLike.DroppedWhile with Transformed[A]
    Definition Classes
    IterableViewLike
  3. trait EmptyView extends Transformed[Nothing] with scala.collection.IterableViewLike.EmptyView
    Definition Classes
    IterableViewLike
  4. trait Filtered extends scala.collection.IterableViewLike.Filtered with Transformed[A]
    Definition Classes
    IterableViewLike
  5. trait FlatMapped[B] extends scala.collection.IterableViewLike.FlatMapped[B] with Transformed[B]
    Definition Classes
    IterableViewLike
  6. trait Forced[B] extends scala.collection.IterableViewLike.Forced[B] with Transformed[B]
    Definition Classes
    IterableViewLike
  7. trait Mapped[B] extends scala.collection.IterableViewLike.Mapped[B] with Transformed[B]
    Definition Classes
    IterableViewLike
  8. trait Prepended[B >: A] extends scala.collection.IterableViewLike.Prepended[B] with Transformed[B]
    Definition Classes
    IterableViewLike
  9. type Self = IterableView[SamRecord, SamSource]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  10. trait Sliced extends scala.collection.IterableViewLike.Sliced with Transformed[A]
    Definition Classes
    IterableViewLike
  11. trait TakenWhile extends scala.collection.IterableViewLike.TakenWhile with Transformed[A]
    Definition Classes
    IterableViewLike
  12. trait Transformed[+B] extends IterableView[B, Coll] with scala.collection.IterableViewLike.Transformed[B]
    Definition Classes
    IterableViewLike
  13. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike
  14. trait Zipped[B] extends Transformed[(A, B)]
    Definition Classes
    IterableViewLike
  15. trait ZippedAll[A1 >: A, B] extends Transformed[(A1, B)]
    Definition Classes
    IterableViewLike

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 SamSource to any2stringadd[SamSource] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: SamRecord, That](xs: GenTraversableOnce[B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  5. def ++:[B >: SamRecord, That](xs: Traversable[B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike
  6. def ++:[B >: SamRecord, That](xs: TraversableOnce[B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike
  7. def ->[B](y: B): (SamSource, B)
    Implicit
    This member is added by an implicit conversion from SamSource to ArrowAssoc[SamSource] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  8. def /:[B](z: B)(op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  9. def :\[B](z: B)(op: (SamRecord, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    ViewMkString
  12. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  13. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  14. def aggregate[B](z: ⇒ B)(seqop: (B, SamRecord) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  15. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  16. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  17. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. def close(): Unit
    Definition Classes
    SamSource → Closeable → AutoCloseable
  19. def collect[B, That](pf: PartialFunction[SamRecord, B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  20. def collectFirst[B](pf: PartialFunction[SamRecord, B]): Option[B]
    Definition Classes
    TraversableOnce
  21. def companion: GenericCompanion[Iterable]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  22. def copyToArray[B >: SamRecord](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  23. def copyToArray[B >: SamRecord](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  24. def copyToArray[B >: SamRecord](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  25. def copyToBuffer[B >: SamRecord](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  26. def count(p: (SamRecord) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  27. def dict: SAMSequenceDictionary

    The sequence dictionary.

    The sequence dictionary.

    Definition Classes
    HeaderHelper
  28. def drop(n: Int): IterableView[SamRecord, SamSource]
    Definition Classes
    IterableViewLike → TraversableViewLike → IterableLike → TraversableLike → GenTraversableLike
  29. def dropRight(n: Int): IterableView[SamRecord, SamSource]
    Definition Classes
    IterableViewLike → IterableLike
  30. def dropWhile(p: (SamRecord) ⇒ Boolean): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  31. def ensuring(cond: (SamSource) ⇒ Boolean, msg: ⇒ Any): SamSource
    Implicit
    This member is added by an implicit conversion from SamSource to Ensuring[SamSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: (SamSource) ⇒ Boolean): SamSource
    Implicit
    This member is added by an implicit conversion from SamSource to Ensuring[SamSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. def ensuring(cond: Boolean, msg: ⇒ Any): SamSource
    Implicit
    This member is added by an implicit conversion from SamSource to Ensuring[SamSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  34. def ensuring(cond: Boolean): SamSource
    Implicit
    This member is added by an implicit conversion from SamSource to Ensuring[SamSource] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  35. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  36. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  37. def exists(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  38. def filter(p: (SamRecord) ⇒ Boolean): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  39. def filterNot(p: (SamRecord) ⇒ Boolean): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  40. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  41. def find(p: (SamRecord) ⇒ Boolean): Option[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  42. def flatMap[B, That](f: (SamRecord) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike → FilterMonadic
  43. def flatten[B](implicit asTraversable: (SamRecord) ⇒ GenTraversableOnce[B]): SamSource.Transformed[B]
    Definition Classes
    TraversableViewLike → GenericTraversableTemplate
  44. def fold[A1 >: SamRecord](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  45. def foldLeft[B](z: B)(op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  46. def foldRight[B](z: B)(op: (SamRecord, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  47. def forall(p: (SamRecord) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  48. def force[B >: SamRecord, That](implicit bf: CanBuildFrom[SamSource, B, That]): That
    Definition Classes
    TraversableViewLike
  49. def foreach[U](f: (SamRecord) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  50. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SamSource to StringFormat[SamSource] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  51. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  52. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  53. def groupBy[K](f: (SamRecord) ⇒ K): Map[K, IterableView[SamRecord, SamSource]]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  54. def grouped(size: Int): Iterator[IterableView[SamRecord, SamSource]]
    Definition Classes
    IterableViewLike → IterableLike
  55. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  56. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  57. def head: SamRecord
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  58. def headOption: Option[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  59. val header: SAMFileHeader

    The htsjdk.samtools.SAMFileHeader associated with the source.

    The htsjdk.samtools.SAMFileHeader associated with the source.

    Definition Classes
    SamSource → HeaderHelper
  60. def indexed: Boolean

    True if an index exists and query() calls can be made, false otherwise.

  61. def init: IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  62. def inits: Iterator[IterableView[SamRecord, SamSource]]
    Definition Classes
    TraversableViewLike → TraversableLike
  63. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  64. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  65. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  66. def iterator: SamIterator

    Returns an iterator over all the records in the source.

    Returns an iterator over all the records in the source.

    Definition Classes
    SamSource → IterableLike → GenIterableLike
  67. def last: SamRecord
    Definition Classes
    TraversableLike → GenTraversableLike
  68. def lastOption: Option[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  69. def map[B, That](f: (SamRecord) ⇒ B)(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike → FilterMonadic
  70. def max[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def maxBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def min[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  73. def minBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    ViewMkString
  75. def mkString(sep: String): String
    Definition Classes
    ViewMkString
  76. def mkString: String
    Definition Classes
    ViewMkString
  77. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  78. def newAppended[B >: SamRecord](that: GenTraversable[B]): Transformed[B]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  79. def newBuilder: Builder[SamRecord, IterableView[SamRecord, SamSource]]
    Attributes
    protected[this]
    Definition Classes
    TraversableViewLike → GenericTraversableTemplate → TraversableLike → HasNewBuilder
  80. def newDropped(n: Int): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  81. def newDroppedWhile(p: (SamRecord) ⇒ Boolean): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  82. def newFiltered(p: (SamRecord) ⇒ Boolean): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  83. def newFlatMapped[B](f: (SamRecord) ⇒ GenTraversableOnce[B]): Transformed[B]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  84. def newForced[B](xs: ⇒ GenSeq[B]): Transformed[B]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  85. def newMapped[B](f: (SamRecord) ⇒ B): Transformed[B]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  86. def newPrepended[B >: SamRecord](that: GenTraversable[B]): Transformed[B]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  87. def newSliced(_endpoints: SliceInterval): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  88. def newTaken(n: Int): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  89. def newTakenWhile(p: (SamRecord) ⇒ Boolean): Transformed[SamRecord]
    Attributes
    protected
    Definition Classes
    IterableViewLike → TraversableViewLike
  90. def newZipped[B](that: GenIterable[B]): Transformed[(SamRecord, B)]
    Attributes
    protected
    Definition Classes
    IterableViewLike
  91. def newZippedAll[A1 >: SamRecord, B](that: GenIterable[B], _thisElem: A1, _thatElem: B): Transformed[(A1, B)]
    Attributes
    protected
    Definition Classes
    IterableViewLike
  92. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  93. final def notify(): Unit
    Definition Classes
    AnyRef
  94. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  95. def par: ParIterable[SamRecord]
    Definition Classes
    Parallelizable
  96. def parCombiner: Combiner[SamRecord, ParIterable[SamRecord]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  97. def partition(p: (SamRecord) ⇒ Boolean): (IterableView[SamRecord, SamSource], IterableView[SamRecord, SamSource])
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  98. def product[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. 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
  100. def query(chrom: String, start: Int, end: Int, queryType: QueryType): SamIterator

    Returns an iterator over the records in the region provided.

  101. def query(regions: TraversableOnce[Locatable], queryType: QueryType = QueryType.Overlapping): SamIterator

    Returns an iterator over the records in the regions provided.

  102. 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
  103. def reduce[A1 >: SamRecord](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def reduceLeft[B >: SamRecord](op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce
  105. def reduceLeftOption[B >: SamRecord](op: (B, SamRecord) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def reduceOption[A1 >: SamRecord](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def reduceRight[B >: SamRecord](op: (SamRecord, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  108. def reduceRightOption[B >: SamRecord](op: (SamRecord, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  109. def repr: IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableLike → GenTraversableLike
  110. def reversed: List[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  111. def sameElements[B >: SamRecord](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  112. def scan[B >: SamRecord, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  113. def scanLeft[B, That](z: B)(op: (B, SamRecord) ⇒ B)(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  114. def scanRight[B, That](z: B)(op: (SamRecord, B) ⇒ B)(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], B, That]): That
    Definition Classes
    TraversableViewLike → 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.

  115. def seq: Iterable[SamRecord]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  116. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  117. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  118. def slice(from: Int, until: Int): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  119. def sliding(size: Int): Iterator[IterableView[SamRecord, SamSource]]
    Definition Classes
    IterableViewLike → IterableLike
  120. def sliding(size: Int, step: Int): Iterator[IterableView[SamRecord, SamSource]]
    Definition Classes
    IterableViewLike → IterableLike
  121. def span(p: (SamRecord) ⇒ Boolean): (IterableView[SamRecord, SamSource], IterableView[SamRecord, SamSource])
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  122. def splitAt(n: Int): (IterableView[SamRecord, SamSource], IterableView[SamRecord, SamSource])
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  123. def stringPrefix: String
    Definition Classes
    IterableViewLike → TraversableViewLike → TraversableLike → GenTraversableLike
  124. def sum[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  125. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  126. def tail: IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  127. def tails: Iterator[IterableView[SamRecord, SamSource]]
    Definition Classes
    TraversableViewLike → TraversableLike
  128. def take(n: Int): IterableView[SamRecord, SamSource]
    Definition Classes
    IterableViewLike → TraversableViewLike → IterableLike → TraversableLike → GenTraversableLike
  129. def takeRight(n: Int): IterableView[SamRecord, SamSource]
    Definition Classes
    IterableViewLike → IterableLike
  130. def takeWhile(p: (SamRecord) ⇒ Boolean): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → GenTraversableLike
  131. def thisCollection: Iterable[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  132. def thisSeq: Seq[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    ViewMkString
  133. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SamRecord, Col[SamRecord]]): Col[SamRecord]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  134. def toArray[B >: SamRecord](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  135. def toBuffer[B >: SamRecord]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  136. def toCollection(repr: IterableView[SamRecord, SamSource]): Iterable[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  137. def toIndexedSeq: IndexedSeq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  138. def toIterable: Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  139. def toIterator: Iterator[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  140. def toList: List[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  141. def toMap[T, U](implicit ev: <:<[SamRecord, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  142. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from SamSource to CollectionsHaveToParArray[SamSource, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (SamSource) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
    CollectionsHaveToParArray
  143. def toSamReader: SamReader

    Returns the underlying SamReader.

    Returns the underlying SamReader. This should be avoided as much as possible, and the SamSource should not be used again after calling toSamReader.

  144. def toSeq: Seq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  145. def toSet[B >: SamRecord]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  146. def toStream: Stream[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  147. def toString(): String

    Provides a string that shows where the source is reading from.

    Provides a string that shows where the source is reading from.

    Definition Classes
    SamSource → TraversableViewLike → TraversableLike → AnyRef → Any
  148. def toTraversable: Traversable[SamRecord]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  149. def toVector: Vector[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  150. def transpose[B](implicit asTraversable: (SamRecord) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  151. def underlying: SamSource

    Required method for IterableView.

    Required method for IterableView.

    Attributes
    protected
    Definition Classes
    SamSource → TraversableViewLike
  152. def unmapped: SamIterator

    Returns an iterator over all the unmapped reads, without positions, at the end of the source.

  153. def unzip[A1, A2](implicit asPair: (SamRecord) ⇒ (A1, A2)): (SamSource.Transformed[A1], SamSource.Transformed[A2])
    Definition Classes
    TraversableViewLike → GenericTraversableTemplate
  154. def unzip3[A1, A2, A3](implicit asTriple: (SamRecord) ⇒ (A1, A2, A3)): (SamSource.Transformed[A1], SamSource.Transformed[A2], SamSource.Transformed[A3])
    Definition Classes
    TraversableViewLike → GenericTraversableTemplate
  155. def view(from: Int, until: Int): IterableView[SamRecord, IterableView[SamRecord, SamSource]]
    Definition Classes
    IterableLike → TraversableLike
  156. def view: IterableView[SamRecord, IterableView[SamRecord, SamSource]]
    Definition Classes
    IterableLike → TraversableLike
  157. def viewIdString: String
    Attributes
    protected[this]
    Definition Classes
    TraversableViewLike
  158. def viewIdentifier: String
    Attributes
    protected[this]
    Definition Classes
    TraversableViewLike
  159. def viewToString: String
    Definition Classes
    TraversableViewLike
  160. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  161. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  162. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  163. def withFilter(p: (SamRecord) ⇒ Boolean): IterableView[SamRecord, SamSource]
    Definition Classes
    TraversableViewLike → TraversableLike → FilterMonadic
  164. def zip[A1 >: SamRecord, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], (A1, B), That]): That
    Definition Classes
    IterableViewLike → IterableLike → GenIterableLike
  165. def zipAll[B, A1 >: SamRecord, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], (A1, B), That]): That
    Definition Classes
    IterableViewLike → IterableLike → GenIterableLike
  166. def zipWithIndex[A1 >: SamRecord, That](implicit bf: CanBuildFrom[IterableView[SamRecord, SamSource], (A1, Int), That]): That
    Definition Classes
    IterableViewLike → IterableLike → GenIterableLike
  167. def →[B](y: B): (SamSource, B)
    Implicit
    This member is added by an implicit conversion from SamSource to ArrowAssoc[SamSource] 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 SamSource 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:
    (samSource: 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 SamSource 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:
    (samSource: 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 SamSource 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:
    (samSource: 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 SamSource 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:
    (samSource: MonadOps[SamRecord]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from Closeable

Inherited from AutoCloseable

Inherited from HeaderHelper

Inherited from IterableView[SamRecord, SamSource]

Inherited from IterableViewLike[SamRecord, SamSource, IterableView[SamRecord, SamSource]]

Inherited from TraversableView[SamRecord, SamSource]

Inherited from TraversableViewLike[SamRecord, SamSource, IterableView[SamRecord, SamSource]]

Inherited from ViewMkString[SamRecord]

Inherited from Iterable[SamRecord]

Inherited from IterableLike[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from Equals

Inherited from GenIterable[SamRecord]

Inherited from GenIterableLike[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from Traversable[SamRecord]

Inherited from GenTraversable[SamRecord]

Inherited from GenericTraversableTemplate[SamRecord, Iterable]

Inherited from TraversableLike[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from GenTraversableLike[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from Parallelizable[SamRecord, ParIterable[SamRecord]]

Inherited from TraversableOnce[SamRecord]

Inherited from GenTraversableOnce[SamRecord]

Inherited from FilterMonadic[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from HasNewBuilder[SamRecord, IterableView[SamRecord, SamSource]]

Inherited from AnyRef

Inherited from Any

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

Inherited by implicit conversion CollectionsHaveToParArray from SamSource to CollectionsHaveToParArray[SamSource, T]

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

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

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

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

Inherited by implicit conversion alternateImplicit from SamSource to ForceImplicitAmbiguity

Ungrouped