class JointVariantContextIterator extends Iterator[Seq[Option[VariantContext]]]
Iterates over multiple variant context iterators such that we return a list of contexts for the union of sites across the iterators. If samples is given, we subset each variant context to just that sample.
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class
GroupedIterator[B >: A] extends AbstractIterator[Seq[B]] with Iterator[Seq[B]]
- Definition Classes
- Iterator
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to any2stringadd[JointVariantContextIterator] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
++[B >: Seq[Option[VariantContext]]](that: ⇒ GenTraversableOnce[B]): Iterator[B]
- Definition Classes
- Iterator
-
def
->[B](y: B): (JointVariantContextIterator, B)
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to ArrowAssoc[JointVariantContextIterator] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
def
/:[B](z: B)(op: (B, Seq[Option[VariantContext]]) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
:\[B](z: B)(op: (Seq[Option[VariantContext]], B) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
addString(b: StringBuilder): StringBuilder
- Definition Classes
- TraversableOnce
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def
addString(b: StringBuilder, sep: String): StringBuilder
- Definition Classes
- TraversableOnce
-
def
addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
- Definition Classes
- TraversableOnce
-
def
aggregate[B](z: ⇒ B)(seqop: (B, Seq[Option[VariantContext]]) ⇒ B, combop: (B, B) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
buffered: BufferedIterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
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- Annotations
- @throws( ... )
-
def
collect[B](pf: PartialFunction[Seq[Option[VariantContext]], B]): Iterator[B]
- Definition Classes
- Iterator
- Annotations
- @migration
- Migration
(Changed in version 2.8.0)
collect
has changed. The previous behavior can be reproduced withtoSeq
.
-
def
collectFirst[B](pf: PartialFunction[Seq[Option[VariantContext]], B]): Option[B]
- Definition Classes
- TraversableOnce
-
def
contains(elem: Any): Boolean
- Definition Classes
- Iterator
-
def
copyToArray[B >: Seq[Option[VariantContext]]](xs: Array[B], start: Int, len: Int): Unit
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
copyToArray[B >: Seq[Option[VariantContext]]](xs: Array[B]): Unit
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
copyToArray[B >: Seq[Option[VariantContext]]](xs: Array[B], start: Int): Unit
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
copyToBuffer[B >: Seq[Option[VariantContext]]](dest: Buffer[B]): Unit
- Definition Classes
- TraversableOnce
-
def
corresponds[B](that: GenTraversableOnce[B])(p: (Seq[Option[VariantContext]], B) ⇒ Boolean): Boolean
- Definition Classes
- Iterator
-
def
count(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Int
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
drop(n: Int): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
dropWhile(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
duplicate: (Iterator[Seq[Option[VariantContext]]], Iterator[Seq[Option[VariantContext]]])
- Definition Classes
- Iterator
-
def
ensuring(cond: (JointVariantContextIterator) ⇒ Boolean, msg: ⇒ Any): JointVariantContextIterator
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to Ensuring[JointVariantContextIterator] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (JointVariantContextIterator) ⇒ Boolean): JointVariantContextIterator
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to Ensuring[JointVariantContextIterator] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): JointVariantContextIterator
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to Ensuring[JointVariantContextIterator] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): JointVariantContextIterator
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to Ensuring[JointVariantContextIterator] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
exists(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Boolean
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
filter(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
filterNot(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
find(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Option[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
flatMap[B](f: (Seq[Option[VariantContext]]) ⇒ GenTraversableOnce[B]): Iterator[B]
- Definition Classes
- Iterator
-
def
flatten: Iterator[Option[VariantContext]]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to FlattenOps[Option[VariantContext]] performed by method flattenTraversableOnce in scala.collection.TraversableOnce.
- Definition Classes
- FlattenOps
-
def
fold[A1 >: Seq[Option[VariantContext]]](z: A1)(op: (A1, A1) ⇒ A1): A1
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
foldLeft[B](z: B)(op: (B, Seq[Option[VariantContext]]) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
foldRight[B](z: B)(op: (Seq[Option[VariantContext]], B) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
forall(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Boolean
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
foreach[U](f: (Seq[Option[VariantContext]]) ⇒ U): Unit
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to StringFormat[JointVariantContextIterator] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
grouped[B >: Seq[Option[VariantContext]]](size: Int): GroupedIterator[B]
- Definition Classes
- Iterator
-
def
hasDefiniteSize: Boolean
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
hasNext(): Boolean
- Definition Classes
- JointVariantContextIterator → Iterator
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
-
def
indexOf[B >: Seq[Option[VariantContext]]](elem: B, from: Int): Int
- Definition Classes
- Iterator
-
def
indexOf[B >: Seq[Option[VariantContext]]](elem: B): Int
- Definition Classes
- Iterator
-
def
indexWhere(p: (Seq[Option[VariantContext]]) ⇒ Boolean, from: Int): Int
- Definition Classes
- Iterator
-
def
indexWhere(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Int
- Definition Classes
- Iterator
-
def
isEmpty: Boolean
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
isTraversableAgain: Boolean
- Definition Classes
- Iterator → GenTraversableOnce
-
def
length: Int
- Definition Classes
- Iterator
-
def
map[B](f: (Seq[Option[VariantContext]]) ⇒ B): Iterator[B]
- Definition Classes
- Iterator
-
def
max[B >: Seq[Option[VariantContext]]](implicit cmp: Ordering[B]): Seq[Option[VariantContext]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
maxBy[B](f: (Seq[Option[VariantContext]]) ⇒ B)(implicit cmp: Ordering[B]): Seq[Option[VariantContext]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
min[B >: Seq[Option[VariantContext]]](implicit cmp: Ordering[B]): Seq[Option[VariantContext]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
minBy[B](f: (Seq[Option[VariantContext]]) ⇒ B)(implicit cmp: Ordering[B]): Seq[Option[VariantContext]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
mkString: String
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
mkString(sep: String): String
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
mkString(start: String, sep: String, end: String): String
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
next(): Seq[Option[VariantContext]]
- Definition Classes
- JointVariantContextIterator → Iterator
-
def
nonEmpty: Boolean
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
-
def
padTo[A1 >: Seq[Option[VariantContext]]](len: Int, elem: A1): Iterator[A1]
- Definition Classes
- Iterator
-
def
partition(p: (Seq[Option[VariantContext]]) ⇒ Boolean): (Iterator[Seq[Option[VariantContext]]], Iterator[Seq[Option[VariantContext]]])
- Definition Classes
- Iterator
-
def
patch[B >: Seq[Option[VariantContext]]](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]
- Definition Classes
- Iterator
-
def
product[B >: Seq[Option[VariantContext]]](implicit num: Numeric[B]): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reduce[A1 >: Seq[Option[VariantContext]]](op: (A1, A1) ⇒ A1): A1
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reduceLeft[B >: Seq[Option[VariantContext]]](op: (B, Seq[Option[VariantContext]]) ⇒ B): B
- Definition Classes
- TraversableOnce
-
def
reduceLeftOption[B >: Seq[Option[VariantContext]]](op: (B, Seq[Option[VariantContext]]) ⇒ B): Option[B]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reduceOption[A1 >: Seq[Option[VariantContext]]](op: (A1, A1) ⇒ A1): Option[A1]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reduceRight[B >: Seq[Option[VariantContext]]](op: (Seq[Option[VariantContext]], B) ⇒ B): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reduceRightOption[B >: Seq[Option[VariantContext]]](op: (Seq[Option[VariantContext]], B) ⇒ B): Option[B]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
reversed: List[Seq[Option[VariantContext]]]
- Attributes
- protected[this]
- Definition Classes
- TraversableOnce
-
def
sameElements(that: Iterator[_]): Boolean
- Definition Classes
- Iterator
-
def
scanLeft[B](z: B)(op: (B, Seq[Option[VariantContext]]) ⇒ B): Iterator[B]
- Definition Classes
- Iterator
-
def
scanRight[B](z: B)(op: (Seq[Option[VariantContext]], B) ⇒ B): Iterator[B]
- Definition Classes
- Iterator
-
def
seq: Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
size: Int
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
sizeHintIfCheap: Int
- Attributes
- protected[scala.collection]
- Definition Classes
- GenTraversableOnce
-
def
slice(from: Int, until: Int): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
sliceIterator(from: Int, until: Int): Iterator[Seq[Option[VariantContext]]]
- Attributes
- protected
- Definition Classes
- Iterator
-
def
sliding[B >: Seq[Option[VariantContext]]](size: Int, step: Int): GroupedIterator[B]
- Definition Classes
- Iterator
-
def
span(p: (Seq[Option[VariantContext]]) ⇒ Boolean): (Iterator[Seq[Option[VariantContext]]], Iterator[Seq[Option[VariantContext]]])
- Definition Classes
- Iterator
-
def
sum[B >: Seq[Option[VariantContext]]](implicit num: Numeric[B]): B
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
take(n: Int): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
takeWhile(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Seq[Option[VariantContext]], Col[Seq[Option[VariantContext]]]]): Col[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toArray[B >: Seq[Option[VariantContext]]](implicit arg0: ClassTag[B]): Array[B]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toBuffer[B >: Seq[Option[VariantContext]]]: Buffer[B]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toIndexedSeq: IndexedSeq[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toIterable: Iterable[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toIterator: Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator → GenTraversableOnce
-
def
toList: List[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toMap[T, U](implicit ev: <:<[Seq[Option[VariantContext]], (T, U)]): Map[T, U]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toParArray: ParArray[T]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to CollectionsHaveToParArray[JointVariantContextIterator, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (JointVariantContextIterator) ⇒ GenTraversableOnce[T] is in scope.
- Definition Classes
- CollectionsHaveToParArray
-
def
toSeq: Seq[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toSet[B >: Seq[Option[VariantContext]]]: Set[B]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
def
toStream: Stream[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator → GenTraversableOnce
-
def
toString(): String
- Definition Classes
- Iterator → AnyRef → Any
-
def
toTraversable: Traversable[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator → TraversableOnce → GenTraversableOnce
-
def
toVector: Vector[Seq[Option[VariantContext]]]
- Definition Classes
- TraversableOnce → GenTraversableOnce
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
withFilter(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Definition Classes
- Iterator
-
def
zip[B](that: Iterator[B]): Iterator[(Seq[Option[VariantContext]], B)]
- Definition Classes
- Iterator
-
def
zipAll[B, A1 >: Seq[Option[VariantContext]], B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]
- Definition Classes
- Iterator
-
def
zipWithIndex: Iterator[(Seq[Option[VariantContext]], Int)]
- Definition Classes
- Iterator
-
def
→[B](y: B): (JointVariantContextIterator, B)
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to ArrowAssoc[JointVariantContextIterator] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
Shadowed Implicit Value Members
-
def
filter(p: (Seq[Option[VariantContext]]) ⇒ Boolean): TraversableOnce[Seq[Option[VariantContext]]]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to MonadOps[Seq[Option[VariantContext]]] 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:(jointVariantContextIterator: MonadOps[Seq[Option[VariantContext]]]).filter(p)
- Definition Classes
- MonadOps
-
def
flatMap[B](f: (Seq[Option[VariantContext]]) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to MonadOps[Seq[Option[VariantContext]]] 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:(jointVariantContextIterator: MonadOps[Seq[Option[VariantContext]]]).flatMap(f)
- Definition Classes
- MonadOps
-
def
map[B](f: (Seq[Option[VariantContext]]) ⇒ B): TraversableOnce[B]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to MonadOps[Seq[Option[VariantContext]]] 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:(jointVariantContextIterator: MonadOps[Seq[Option[VariantContext]]]).map(f)
- Definition Classes
- MonadOps
-
def
withFilter(p: (Seq[Option[VariantContext]]) ⇒ Boolean): Iterator[Seq[Option[VariantContext]]]
- Implicit
- This member is added by an implicit conversion from JointVariantContextIterator to MonadOps[Seq[Option[VariantContext]]] 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:(jointVariantContextIterator: MonadOps[Seq[Option[VariantContext]]]).withFilter(p)
- Definition Classes
- MonadOps