Packages

class FilterSomaticVcf extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. FilterSomaticVcf
  2. LazyLogging
  3. FgBioTool
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new FilterSomaticVcf(input: FgBioDef.PathToVcf, output: FgBioDef.PathToVcf, bam: FgBioDef.PathToBam, sample: Option[String] = None, minMappingQuality: Int = 30, minBaseQuality: Int = 20, pairedReadsOnly: Boolean = false, endRepairDistance: Int = 2, endRepairPValue: Option[Double] = None)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to any2stringadd[FilterSomaticVcf] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (FilterSomaticVcf, B)
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to ArrowAssoc[FilterSomaticVcf] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. val bam: FgBioDef.PathToBam
  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. val endRepairDistance: Int
  10. val endRepairPValue: Option[Double]
  11. def ensuring(cond: (FilterSomaticVcf) ⇒ Boolean, msg: ⇒ Any): FilterSomaticVcf
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to Ensuring[FilterSomaticVcf] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: (FilterSomaticVcf) ⇒ Boolean): FilterSomaticVcf
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to Ensuring[FilterSomaticVcf] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean, msg: ⇒ Any): FilterSomaticVcf
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to Ensuring[FilterSomaticVcf] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: Boolean): FilterSomaticVcf
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to Ensuring[FilterSomaticVcf] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. def execute(): Unit
    Definition Classes
    FilterSomaticVcf → FgBioTool
  18. def fail(exit: Int, message: String): Nothing

    Fail with a specific error code and message.

    Fail with a specific error code and message.

    Definition Classes
    FgBioTool
  19. def fail(message: String): Nothing

    Fail with the default exit code and a message.

    Fail with the default exit code and a message.

    Definition Classes
    FgBioTool
  20. def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool
  21. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  22. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to StringFormat[FilterSomaticVcf] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  23. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  24. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  25. val input: FgBioDef.PathToVcf
  26. def invalid(message: String): Nothing

    Generates a new validation exception with the given message.

    Generates a new validation exception with the given message.

    Definition Classes
    FgBioTool
  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  29. val minBaseQuality: Int
  30. val minMappingQuality: Int
  31. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  32. final def notify(): Unit
    Definition Classes
    AnyRef
  33. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  34. val output: FgBioDef.PathToVcf
  35. val pairedReadsOnly: Boolean
  36. val sample: Option[String]
  37. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  38. def toString(): String
    Definition Classes
    AnyRef → Any
  39. def validate(test: Boolean, message: ⇒ String): Unit

    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes
    FgBioTool
  40. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  41. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  42. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  43. def →[B](y: B): (FilterSomaticVcf, B)
    Implicit
    This member is added by an implicit conversion from FilterSomaticVcf to ArrowAssoc[FilterSomaticVcf] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from LazyLogging

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from FilterSomaticVcf to any2stringadd[FilterSomaticVcf]

Inherited by implicit conversion StringFormat from FilterSomaticVcf to StringFormat[FilterSomaticVcf]

Inherited by implicit conversion Ensuring from FilterSomaticVcf to Ensuring[FilterSomaticVcf]

Inherited by implicit conversion ArrowAssoc from FilterSomaticVcf to ArrowAssoc[FilterSomaticVcf]

Ungrouped