Packages

c

com.fulcrumgenomics.personal.nhomer

GenerateRegionsFromFasta

class GenerateRegionsFromFasta extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. GenerateRegionsFromFasta
  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 GenerateRegionsFromFasta(input: commons.CommonsDef.PathToFasta, output: Path = Io.StdOut, regionSize: Int = 100000)

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 GenerateRegionsFromFasta to any2stringadd[GenerateRegionsFromFasta] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (GenerateRegionsFromFasta, B)
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to ArrowAssoc[GenerateRegionsFromFasta] 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. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def ensuring(cond: (GenerateRegionsFromFasta) ⇒ Boolean, msg: ⇒ Any): GenerateRegionsFromFasta
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to Ensuring[GenerateRegionsFromFasta] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  9. def ensuring(cond: (GenerateRegionsFromFasta) ⇒ Boolean): GenerateRegionsFromFasta
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to Ensuring[GenerateRegionsFromFasta] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: Boolean, msg: ⇒ Any): GenerateRegionsFromFasta
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to Ensuring[GenerateRegionsFromFasta] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean): GenerateRegionsFromFasta
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to Ensuring[GenerateRegionsFromFasta] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  14. def execute(): Unit
    Definition Classes
    GenerateRegionsFromFastaFgBioTool
  15. 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
  16. 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
  17. def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool
  18. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  19. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to StringFormat[GenerateRegionsFromFasta] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  21. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  22. val input: commons.CommonsDef.PathToFasta
  23. 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
  24. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  25. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  26. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. final def notify(): Unit
    Definition Classes
    AnyRef
  28. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  29. val output: Path
  30. val regionSize: Int
  31. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  32. def toString(): String
    Definition Classes
    AnyRef → Any
  33. 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
  34. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  35. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  36. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. def [B](y: B): (GenerateRegionsFromFasta, B)
    Implicit
    This member is added by an implicit conversion from GenerateRegionsFromFasta to ArrowAssoc[GenerateRegionsFromFasta] 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 GenerateRegionsFromFasta to any2stringadd[GenerateRegionsFromFasta]

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

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

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

Ungrouped