class FgBioDef extends CommonsDef
Place to put common function, type and implicit definitions that can be imported into other classes easily.
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Instance Constructors
- new FgBioDef()
Type Members
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implicit
class
BetterBufferedIteratorJavaWrapper
[A] extends AnyRef
Implicit class that provides a method to wrap a Java iterator into a BetterBufferedIterator.
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implicit
class
BetterBufferedIteratorScalaWrapper
[A] extends AnyRef
Implicit class that provides a method to wrap an iterator into a BetterBufferedIterator.
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type
DirPath = Path
- Definition Classes
- CommonsDef
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trait
DualIterator
[A] extends Iterator[A] with Iterator[A]
A trait that combine's scala's Iterator with Java's Iterator.
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type
FilePath = Path
- Definition Classes
- CommonsDef
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type
FilenamePrefix = String
- Definition Classes
- CommonsDef
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implicit
class
IteratorToJavaCollectionsAdapter
[A] extends AnyRef
Implicit class that provides methods for creating Java collections from an Iterator.
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implicit
class
ParSupport
[A, B <: ParIterableLike[_, _, _]] extends AnyRef
Implicit that provides additional methods to any collection that is Parallelizable.
Implicit that provides additional methods to any collection that is Parallelizable. Introduces parWith() methods that create parallel versions of the collection with various configuration options.
- A
the type of the elements in the collection
- B
the type of the parallel representation of the collection
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type
PathPrefix = Path
- Definition Classes
- CommonsDef
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type
PathToBam = Path
- Definition Classes
- CommonsDef
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type
PathToFasta = Path
- Definition Classes
- CommonsDef
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type
PathToFastq = Path
- Definition Classes
- CommonsDef
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type
PathToIntervals = Path
- Definition Classes
- CommonsDef
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type
PathToVcf = Path
- Definition Classes
- CommonsDef
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implicit
class
SafelyClosable extends AnyRef
- Definition Classes
- CommonsDef
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
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- def +(other: String): String
- def ->[B](y: B): (FgBioDef, B)
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
- Definition Classes
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- def ensuring(cond: (FgBioDef) ⇒ Boolean, msg: ⇒ Any): FgBioDef
- def ensuring(cond: (FgBioDef) ⇒ Boolean): FgBioDef
- def ensuring(cond: Boolean, msg: ⇒ Any): FgBioDef
- def ensuring(cond: Boolean): FgBioDef
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
- Attributes
- protected[java.lang]
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- @throws( classOf[java.lang.Throwable] )
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def
forloop[T](from: T)(check: (T) ⇒ Boolean)(next: (T) ⇒ T)(f: (T) ⇒ Unit): Unit
A more generic for loop, that gives performance similar, but slightly worse than, FgBioDef#forloop(Int,Int,Int).
A more generic for loop, that gives performance similar, but slightly worse than, FgBioDef#forloop(Int,Int,Int). Equivalent to:
for (i=from; check(i); i=next(i)) f(i)
- T
the type of the index
- from
an initial value
- check
a function that checks to see if a value should be evaluated (not cause termination)
- next
a function that takes a value and produced the next value
- f
a function called on all values
- Annotations
- @inline()
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def
forloop(from: Int, until: Int, by: Int = 1)(f: (Int) ⇒ Unit): Unit
An implementation of a for loop that has performance similar to writing a custom while loop for primitive types, which suffer great performance loss when iterating via foreach(), and especially with zipWithIndex.foreach().
An implementation of a for loop that has performance similar to writing a custom while loop for primitive types, which suffer great performance loss when iterating via foreach(), and especially with zipWithIndex.foreach().
Equivalent to: for(int i=from; i<until; i+=by) f(i)
- from
an initial integer values
- until
a value one higher than the last value that should be accepted
- by
a step value to increment by each iteration
- f
a function that takes the index and is called each iteration
- Annotations
- @inline()
- def formatted(fmtstr: String): String
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final
def
getClass(): Class[_]
- Definition Classes
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def
hashCode(): Int
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
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implicit
def
javaIterableToIterator[A](iterable: Iterable[A]): Iterator[A]
Implicit that converts a Java Iterable into a scala Iterator.
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implicit
def
javaIteratorAsScalaIterator[A](iterator: Iterator[A]): DualIterator[A]
Implicit that wraps a Java iterator as a Scala iterator.
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
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implicit
def
scalaIteratorAsJavaIterator[A](iterator: Iterator[A]): DualIterator[A]
Implicit that wraps a Scala iterator as a Java iterator.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
- Definition Classes
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def
tryWith[A, B](resource: A, logger: Option[Logger])(cleanup: (A) ⇒ Unit)(doWork: (A) ⇒ B): Try[B]
- Definition Classes
- CommonsDef
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def
tryWithCloseable[A <: Closeable](resource: A, logger: Option[Logger])(doWork: (A) ⇒ Unit): Try[Unit]
- Definition Classes
- CommonsDef
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def
unreachable(message: ⇒ String): Nothing
- Definition Classes
- CommonsDef
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final
def
wait(): Unit
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- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- Annotations
- @throws( ... )
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def
yieldAndThen[A](it: ⇒ A)(block: ⇒ Unit): A
- Definition Classes
- CommonsDef
- def →[B](y: B): (FgBioDef, B)