Packages

trait SimpleRead extends AnyRef

A trait that consensus reads must implement.

Linear Supertypes
AnyRef, Any
Known Subclasses
DuplexConsensusRead, SourceRead, VanillaConsensusRead
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SimpleRead
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def bases: Array[Byte]

    The bases of the consensus read.

  2. abstract def id: String

    The ID of the molecule that generated the consensus read.

  3. abstract def quals: Array[Byte]

    The quals of the consensus read.

Concrete 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 SimpleRead to any2stringadd[SimpleRead] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (SimpleRead, B)
    Implicit
    This member is added by an implicit conversion from SimpleRead to ArrowAssoc[SimpleRead] 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 baseString: String

    Returns the consensus read a String - mostly useful for testing.

  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. def ensuring(cond: (SimpleRead) ⇒ Boolean, msg: ⇒ Any): SimpleRead
    Implicit
    This member is added by an implicit conversion from SimpleRead to Ensuring[SimpleRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (SimpleRead) ⇒ Boolean): SimpleRead
    Implicit
    This member is added by an implicit conversion from SimpleRead to Ensuring[SimpleRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): SimpleRead
    Implicit
    This member is added by an implicit conversion from SimpleRead to Ensuring[SimpleRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): SimpleRead
    Implicit
    This member is added by an implicit conversion from SimpleRead to Ensuring[SimpleRead] 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 finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SimpleRead to StringFormat[SimpleRead] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  19. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  20. def length: Int

    Gets the length of the consensus read.

  21. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  22. final def notify(): Unit
    Definition Classes
    AnyRef
  23. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  24. def qualString: String

    Retrieves the quals as a phred+33/fastq ascii String.

  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  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( ... )
  30. def →[B](y: B): (SimpleRead, B)
    Implicit
    This member is added by an implicit conversion from SimpleRead to ArrowAssoc[SimpleRead] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped