Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

   AnyRef → Any

3.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

4.  var DefaultUseAsyncIo: Boolean
5.  var DefaultValidationStringency: ValidationStringency
6.  def apply(path: FgBioDef.PathToBam, index: Option[FgBioDef.FilePath] = None, ref: Option[FgBioDef.PathToFasta] = None, async: Boolean = DefaultUseAsyncIo, stringency: ValidationStringency = DefaultValidationStringency, factory: SAMRecordFactory = SamRecord.Factory): SamSource

   Constructs a SamSource to read from the provided path.

   Constructs a SamSource to read from the provided path.

   path

   the path to read the SAM/BAM/CRAM from

   index

   an optional path to read the index from

   ref

   an optional reference sequencing for decoding CRAM files

   async

   if true use extra thread(s) to speed up reading

   stringency

   the validation stringency to apply when reading the data

   factory

   a SAMRecordFactory; MUST return classes that mix in SamRecord

7.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

9.  final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

10.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

11.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

12.  final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

13.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

14.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

15.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

16.  final def notify(): Unit

    Definition Classes

    AnyRef

17.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

18.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

19.  def toString(): String

    Definition Classes

    AnyRef → Any

20.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

21.  final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

22.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )