Packages

case class SourceRead(id: String, bases: Array[Byte], quals: Array[Byte], cigar: Cigar, sam: Option[SamRecord] = None) extends SimpleRead with Product with Serializable

Stores information about a read to be fed into a consensus.

Linear Supertypes
Serializable, Serializable, Product, Equals, SimpleRead, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SourceRead
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. SimpleRead
  7. AnyRef
  8. 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 SourceRead(id: String, bases: Array[Byte], quals: Array[Byte], cigar: Cigar, sam: Option[SamRecord] = 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 SourceRead to any2stringadd[SourceRead] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (SourceRead, B)
    Implicit
    This member is added by an implicit conversion from SourceRead to ArrowAssoc[SourceRead] 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.

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

    Definition Classes
    SimpleRead
  8. val bases: Array[Byte]

    The bases of the consensus read.

    The bases of the consensus read.

    Definition Classes
    SourceRead → SimpleRead
  9. val cigar: Cigar
  10. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  11. def ensuring(cond: (SourceRead) ⇒ Boolean, msg: ⇒ Any): SourceRead
    Implicit
    This member is added by an implicit conversion from SourceRead to Ensuring[SourceRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: (SourceRead) ⇒ Boolean): SourceRead
    Implicit
    This member is added by an implicit conversion from SourceRead to Ensuring[SourceRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean, msg: ⇒ Any): SourceRead
    Implicit
    This member is added by an implicit conversion from SourceRead to Ensuring[SourceRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: Boolean): SourceRead
    Implicit
    This member is added by an implicit conversion from SourceRead to Ensuring[SourceRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  17. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SourceRead to StringFormat[SourceRead] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  19. val id: String

    The ID of the molecule that generated the consensus read.

    The ID of the molecule that generated the consensus read.

    Definition Classes
    SourceRead → SimpleRead
  20. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  21. def length: Int

    Gets the length of the consensus read.

    Gets the length of the consensus read.

    Definition Classes
    SimpleRead
  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  24. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  25. def qualString: String

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

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

    Definition Classes
    SimpleRead
  26. val quals: Array[Byte]

    The quals of the consensus read.

    The quals of the consensus read.

    Definition Classes
    SourceRead → SimpleRead
  27. val sam: Option[SamRecord]
  28. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  29. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  32. def →[B](y: B): (SourceRead, B)
    Implicit
    This member is added by an implicit conversion from SourceRead to ArrowAssoc[SourceRead] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from SimpleRead

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped