object FgBioDef extends CommonsDef
FgBioDef that is just an extension of the commons CommonsDef. Here in case there's a need for FgBio specific defs later.
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implicit
class
BetterBufferedIteratorJavaWrapper[A] extends AnyRef
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- CommonsDef
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implicit
class
BetterBufferedIteratorScalaWrapper[A] extends AnyRef
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type
DirPath = Path
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trait
DualIterator[A] extends Iterator[A] with Iterator[A]
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trait
FgBioEnum
[T <: EnumEntry] extends Enum[T]
Extends this trait in your enumeration object to enable the case objects to be created on the command line.
Extends this trait in your enumeration object to enable the case objects to be created on the command line. You should implement the Enum#values method in your object, for example:
def values: IndexedSeq[T] = findValues
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type
FilePath = Path
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type
FilenamePrefix = String
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implicit
class
IteratorToJavaCollectionsAdapter[A] extends AnyRef
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implicit
class
ParSupport[A, B <: ParIterableLike[_, _, _]] extends AnyRef
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type
PathPrefix = Path
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type
PathToBam = Path
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type
PathToFasta = Path
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type
PathToFastq = Path
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type
PathToIntervals = Path
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type
PathToVcf = Path
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implicit
class
SafelyClosable extends AnyRef
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implicit
class
SumBy[A] extends AnyRef
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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def
forloop[T](from: T)(check: (T) ⇒ Boolean)(next: (T) ⇒ T)(f: (T) ⇒ Unit): Unit
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def
forloop(from: Int, until: Int, by: Int)(f: (Int) ⇒ Unit): Unit
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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implicit
def
javaIterableToIterator[A](iterable: Iterable[A]): Iterator[A]
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implicit
def
javaIteratorAsScalaIterator[A](iterator: Iterator[A]): DualIterator[A]
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
plotDescription(reader: SamSource, input: FilePath): String
Gets a description for use in a generating a plot.
Gets a description for use in a generating a plot. Returns the
<sample> / <library>
if there is only one sample and library, otherwise the input file name. -
implicit
def
scalaIteratorAsJavaIterator[A](iterator: Iterator[A]): DualIterator[A]
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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def
tryWith[A, B](resource: A, logger: Option[Logger])(cleanup: (A) ⇒ Unit)(doWork: (A) ⇒ B): Try[B]
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def
tryWithCloseable[A <: Closeable](resource: A, logger: Option[Logger])(doWork: (A) ⇒ Unit): Try[Unit]
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def
unreachable(message: ⇒ String): Nothing
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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def
yieldAndThen[A](it: ⇒ A)(block: ⇒ Unit): A
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