Class

com.fulcrumgenomics.umi.UmiConsensusCaller

SourceRead

Related Doc: package UmiConsensusCaller

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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
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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)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. def +(other: String): String

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    Implicit information
    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)

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    Implicit information
    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

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    Definition Classes
    AnyRef → Any

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def baseString: String

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    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]

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    The bases of the consensus read.

    The bases of the consensus read.

    Definition Classes
    SourceRead → SimpleRead

  9. val cigar: Cigar

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  10. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  11. def ensuring(cond: (SourceRead) ⇒ Boolean, msg: ⇒ Any): SourceRead

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    Implicit information
    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

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    Implicit information
    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

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    Implicit information
    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

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    Implicit information
    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

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    Definition Classes
    AnyRef

  16. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  17. def formatted(fmtstr: String): String

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    Implicit information
    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[_]

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    Definition Classes
    AnyRef → Any

  19. val id: String

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    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

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    Definition Classes
    Any

  21. def length: Int

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    Gets the length of the consensus read.

    Gets the length of the consensus read.

    Definition Classes
    SimpleRead

  22. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  23. final def notify(): Unit

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    Definition Classes
    AnyRef

  24. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  25. def qualString: String

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    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]

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    The quals of the consensus read.

    The quals of the consensus read.

    Definition Classes
    SourceRead → SimpleRead

  27. val sam: Option[SamRecord]

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  28. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  29. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  30. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  31. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  32. def →[B](y: B): (SourceRead, B)

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    Implicit information
    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