Class

com.fulcrumgenomics.umi.DuplexConsensusCaller

DuplexConsensusRead

Related Doc: package DuplexConsensusCaller

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case class DuplexConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], errors: Array[Short], abConsensus: VanillaConsensusRead, baConsensus: Option[VanillaConsensusRead]) extends SimpleRead with Product with Serializable

Stores information about a consensus read. Bases, arrays, and the two single strand consensus reads (when present) must all be the same length.

bases

the base calls of the consensus read

quals

the calculated phred-scaled quality scores of the bases

errors

the total number of raw read errors vs. the final consensus sequence at each base

abConsensus

the AB consensus read from which the duplex was constructed

baConsensus

the BA consensus read from which the duplex was constructed, if present. It may not be present if created from the AB strand reads only.

Linear Supertypes
Serializable, Serializable, Product, Equals, SimpleRead, AnyRef, Any
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Inherited
  1. DuplexConsensusRead
  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 DuplexConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], errors: Array[Short], abConsensus: VanillaConsensusRead, baConsensus: Option[VanillaConsensusRead])

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    bases

    the base calls of the consensus read

    quals

    the calculated phred-scaled quality scores of the bases

    errors

    the total number of raw read errors vs. the final consensus sequence at each base

    abConsensus

    the AB consensus read from which the duplex was constructed

    baConsensus

    the BA consensus read from which the duplex was constructed, if present. It may not be present if created from the AB strand reads only.

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 DuplexConsensusRead to any2stringadd[DuplexConsensusRead] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  4. def ->[B](y: B): (DuplexConsensusRead, B)

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to ArrowAssoc[DuplexConsensusRead] 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. val abConsensus: VanillaConsensusRead

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    the AB consensus read from which the duplex was constructed

  7. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  8. val baConsensus: Option[VanillaConsensusRead]

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    the BA consensus read from which the duplex was constructed, if present.

    the BA consensus read from which the duplex was constructed, if present. It may not be present if created from the AB strand reads only.

  9. 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

  10. val bases: Array[Byte]

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    the base calls of the consensus read

    the base calls of the consensus read

    Definition Classes
    DuplexConsensusRead → SimpleRead

  11. def clone(): AnyRef

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

  12. def ensuring(cond: (DuplexConsensusRead) ⇒ Boolean, msg: ⇒ Any): DuplexConsensusRead

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  13. def ensuring(cond: (DuplexConsensusRead) ⇒ Boolean): DuplexConsensusRead

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  14. def ensuring(cond: Boolean, msg: ⇒ Any): DuplexConsensusRead

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  15. def ensuring(cond: Boolean): DuplexConsensusRead

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to Ensuring[DuplexConsensusRead] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  16. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  17. val errors: Array[Short]

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    the total number of raw read errors vs.

    the total number of raw read errors vs. the final consensus sequence at each base

  18. def finalize(): Unit

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

  19. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to StringFormat[DuplexConsensusRead] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  20. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  21. 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
    DuplexConsensusRead → SimpleRead

  22. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  23. def length: Int

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    Gets the length of the consensus read.

    Gets the length of the consensus read.

    Definition Classes
    SimpleRead

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

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    Definition Classes
    AnyRef

  25. final def notify(): Unit

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    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  27. 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

  28. val quals: Array[Byte]

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    the calculated phred-scaled quality scores of the bases

    the calculated phred-scaled quality scores of the bases

    Definition Classes
    DuplexConsensusRead → SimpleRead

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

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    Definition Classes
    AnyRef

  30. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  33. def →[B](y: B): (DuplexConsensusRead, B)

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    Implicit information
    This member is added by an implicit conversion from DuplexConsensusRead to ArrowAssoc[DuplexConsensusRead] 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 DuplexConsensusRead to any2stringadd[DuplexConsensusRead]

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

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

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

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