class SamSource extends Iterable[SamRecord] with HeaderHelper with Closeable

A source class for reading SAM/BAM/CRAM files and for querying them.

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Inherited
  1. SamSource
  2. Closeable
  3. AutoCloseable
  4. HeaderHelper
  5. Iterable
  6. IterableLike
  7. Equals
  8. GenIterable
  9. GenIterableLike
  10. Traversable
  11. GenTraversable
  12. GenericTraversableTemplate
  13. TraversableLike
  14. GenTraversableLike
  15. Parallelizable
  16. TraversableOnce
  17. GenTraversableOnce
  18. FilterMonadic
  19. HasNewBuilder
  20. AnyRef
  21. Any
Implicitly
  1. by MonadOps
  2. by CollectionsHaveToParArray
  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
  7. by alternateImplicit
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Visibility
  1. Public
  2. All

Type Members

  1. type Self = Iterable[SamRecord]
    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 +(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](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: SamRecord, That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: SamRecord, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    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): StringBuilder
    Definition Classes
    TraversableOnce
  12. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  13. def addString(b: StringBuilder, start: String, sep: String, end: 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[Iterable[SamRecord], B, That]): That
    Definition Classes
    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): Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  29. def dropRight(n: Int): Iterable[SamRecord]
    Definition Classes
    IterableLike
  30. def dropWhile(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]
    Definition Classes
    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): Iterable[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  39. def filterNot(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]
    Definition Classes
    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[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  43. def flatten[B](implicit asTraversable: (SamRecord) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    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 foreach[U](f: (SamRecord) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  49. 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()
  50. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  51. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  52. def groupBy[K](f: (SamRecord) ⇒ K): Map[K, Iterable[SamRecord]]
    Definition Classes
    TraversableLike → GenTraversableLike
  53. def grouped(size: Int): Iterator[Iterable[SamRecord]]
    Definition Classes
    IterableLike
  54. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  55. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  56. def head: SamRecord
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  57. def headOption: Option[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  58. val header: SAMFileHeader

    The htsjdk.samtools.SAMFileHeader associated with the source.

    The htsjdk.samtools.SAMFileHeader associated with the source.

    Definition Classes
    SamSource → HeaderHelper
  59. def indexed: Boolean

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

  60. def init: Iterable[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  61. def inits: Iterator[Iterable[SamRecord]]
    Definition Classes
    TraversableLike
  62. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  63. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  64. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  65. 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
  66. def last: SamRecord
    Definition Classes
    TraversableLike → GenTraversableLike
  67. def lastOption: Option[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  68. def map[B, That](f: (SamRecord) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  69. def max[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  70. def maxBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def min[B >: SamRecord](implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def minBy[B](f: (SamRecord) ⇒ B)(implicit cmp: Ordering[B]): SamRecord
    Definition Classes
    TraversableOnce → GenTraversableOnce
  73. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  75. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  76. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  77. def newBuilder: Builder[SamRecord, Iterable[SamRecord]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  78. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  79. final def notify(): Unit
    Definition Classes
    AnyRef
  80. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  81. def par: ParIterable[SamRecord]
    Definition Classes
    Parallelizable
  82. def parCombiner: Combiner[SamRecord, ParIterable[SamRecord]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  83. def partition(p: (SamRecord) ⇒ Boolean): (Iterable[SamRecord], Iterable[SamRecord])
    Definition Classes
    TraversableLike → GenTraversableLike
  84. def product[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. 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
  86. def query(chrom: String, start: Int, end: Int, queryType: QueryType): SamIterator

    Returns an iterator over the records in the region provided.

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

    Returns an iterator over the records in the regions provided.

  88. 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
  89. def reduce[A1 >: SamRecord](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. def reduceLeft[B >: SamRecord](op: (B, SamRecord) ⇒ B): B
    Definition Classes
    TraversableOnce
  91. def reduceLeftOption[B >: SamRecord](op: (B, SamRecord) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  92. def reduceOption[A1 >: SamRecord](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  93. def reduceRight[B >: SamRecord](op: (SamRecord, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  94. def reduceRightOption[B >: SamRecord](op: (SamRecord, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  95. def repr: Iterable[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  96. def reversed: List[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  97. def sameElements[B >: SamRecord](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  98. def scan[B >: SamRecord, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  99. def scanLeft[B, That](z: B)(op: (B, SamRecord) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  100. def scanRight[B, That](z: B)(op: (SamRecord, B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[SamRecord], 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.

  101. def seq: Iterable[SamRecord]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  102. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  104. def slice(from: Int, until: Int): Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  105. def sliding(size: Int, step: Int): Iterator[Iterable[SamRecord]]
    Definition Classes
    IterableLike
  106. def sliding(size: Int): Iterator[Iterable[SamRecord]]
    Definition Classes
    IterableLike
  107. def span(p: (SamRecord) ⇒ Boolean): (Iterable[SamRecord], Iterable[SamRecord])
    Definition Classes
    TraversableLike → GenTraversableLike
  108. def splitAt(n: Int): (Iterable[SamRecord], Iterable[SamRecord])
    Definition Classes
    TraversableLike → GenTraversableLike
  109. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  110. def sum[B >: SamRecord](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  111. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  112. def tail: Iterable[SamRecord]
    Definition Classes
    TraversableLike → GenTraversableLike
  113. def tails: Iterator[Iterable[SamRecord]]
    Definition Classes
    TraversableLike
  114. def take(n: Int): Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  115. def takeRight(n: Int): Iterable[SamRecord]
    Definition Classes
    IterableLike
  116. def takeWhile(p: (SamRecord) ⇒ Boolean): Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  117. def thisCollection: Iterable[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  118. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SamRecord, Col[SamRecord]]): Col[SamRecord]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  119. def toArray[B >: SamRecord](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  120. def toBuffer[B >: SamRecord]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  121. def toCollection(repr: Iterable[SamRecord]): Iterable[SamRecord]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  122. def toIndexedSeq: IndexedSeq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  123. def toIterable: Iterable[SamRecord]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  124. def toIterator: Iterator[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  125. def toList: List[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  126. def toMap[T, U](implicit ev: <:<[SamRecord, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  127. 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
  128. 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.

  129. def toSeq: Seq[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  130. def toSet[B >: SamRecord]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  131. def toStream: Stream[SamRecord]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  132. 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 → TraversableLike → AnyRef → Any
  133. def toTraversable: Traversable[SamRecord]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  134. def toVector: Vector[SamRecord]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  135. 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.

  136. def unmapped: SamIterator

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

  137. def unzip[A1, A2](implicit asPair: (SamRecord) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
    GenericTraversableTemplate
  138. def unzip3[A1, A2, A3](implicit asTriple: (SamRecord) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
    GenericTraversableTemplate
  139. def view(from: Int, until: Int): IterableView[SamRecord, Iterable[SamRecord]]
    Definition Classes
    IterableLike → TraversableLike
  140. def view: IterableView[SamRecord, Iterable[SamRecord]]
    Definition Classes
    IterableLike → TraversableLike
  141. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  142. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  143. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  144. def withFilter(p: (SamRecord) ⇒ Boolean): FilterMonadic[SamRecord, Iterable[SamRecord]]
    Definition Classes
    TraversableLike → FilterMonadic
  145. def zip[A1 >: SamRecord, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  146. def zipAll[B, A1 >: SamRecord, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  147. def zipWithIndex[A1 >: SamRecord, That](implicit bf: CanBuildFrom[Iterable[SamRecord], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  148. 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 Iterable[SamRecord]

Inherited from Equals

Inherited from GenIterable[SamRecord]

Inherited from Traversable[SamRecord]

Inherited from GenTraversable[SamRecord]

Inherited from Parallelizable[SamRecord, ParIterable[SamRecord]]

Inherited from TraversableOnce[SamRecord]

Inherited from GenTraversableOnce[SamRecord]

Inherited from HasNewBuilder[SamRecord, Iterable[com.fulcrumgenomics.bam.api.SamRecord] @scala.annotation.unchecked.uncheckedVariance]

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