ca.innovativemedicine.vcf.app

Flatten

object Flatten extends App

This application is used to "flatten" a VCF file. That is, it expands the INFO fields and the sample data to their own individual columns. To deal with multiple samples, it can create a new, separate, TSV file for each sample.

Linear Supertypes
App, DelayedInit, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. Flatten
  2. App
  3. DelayedInit
  4. AnyRef
  5. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. def args: Array[String]

    Attributes
    protected
    Definition Classes
    App

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. def delayedInit(body: ⇒ Unit): Unit

    Definition Classes
    App → DelayedInit

  10. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  11. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  12. val executionStart: Long

    Definition Classes
    App

  13. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  14. def flatten(params: FlattenParams): (VcfInfo, Iterator[(Variant, List[Format], List[List[List[VcfValue]]])]) ⇒ Either[String, Unit]

    Returns a Reader for a given set of parameters that will output a set of flattened files.

  15. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  16. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  18. def main(args: Array[String]): Unit

    Definition Classes
    App

  19. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. def parseArgs(params: FlattenParams, args: List[String]): Option[FlattenParams]

    Annotations
    @tailrec()

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

    Definition Classes
    AnyRef

  24. def toString(): String

    Definition Classes
    AnyRef → Any

  25. def usage(): Unit

  26. def usageString: String

  27. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  29. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from App

Inherited from DelayedInit

Inherited from AnyRef

Inherited from Any

Ungrouped