c

com.fulcrumgenomics.bam

FindTechnicalReads

class FindTechnicalReads extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. FindTechnicalReads
  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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  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new FindTechnicalReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, matchLength: Int = 15, maxErrors: Int = 1, sequences: Seq[String] = ..., allReads: Boolean = false, tag: Option[String] = 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 FindTechnicalReads to any2stringadd[FindTechnicalReads] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (FindTechnicalReads, B)
    Implicit
    This member is added by an implicit conversion from FindTechnicalReads to ArrowAssoc[FindTechnicalReads] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. val allReads: Boolean
  7. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. def ensuring(cond: (FindTechnicalReads) ⇒ Boolean, msg: ⇒ Any): FindTechnicalReads
    Implicit
    This member is added by an implicit conversion from FindTechnicalReads to Ensuring[FindTechnicalReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (FindTechnicalReads) ⇒ Boolean): FindTechnicalReads
    Implicit
    This member is added by an implicit conversion from FindTechnicalReads to Ensuring[FindTechnicalReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): FindTechnicalReads
    Implicit
    This member is added by an implicit conversion from FindTechnicalReads to Ensuring[FindTechnicalReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): FindTechnicalReads
    Implicit
    This member is added by an implicit conversion from FindTechnicalReads to Ensuring[FindTechnicalReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  15. def execute(): Unit
    Definition Classes
    FindTechnicalReads → FgBioTool
  16. 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
  17. 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
  18. def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

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

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

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

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

Ungrouped