class ConsensusCaller extends AnyRef

Generic consensus caller class that can be used to produce consensus base calls and qualities from a pileup of raw base calls and qualities.

The consensus caller sees the process of going from a DNA source molecule in its original, pristine, state to a sequenced base as having three phases each with their own distinct error profiles: 1) The phase whereby the source molecule is harvested (e.g. cells extracted and lysed) to the point where some kind of molecular identifier has been attached that will allow for identification of replicates that are generated from the same original source molecule. Errors in this phase will be present in all copies of the molecule that are prepared for sequencing (except where a second error reverts the change).

2) Everything between phases 1 & 3! Generally including any sample preparation activities after a molecular identifier has been attached but prior to sequencing. Errors introduced in this phase will be present in some fraction of the molecules available at sequencing.

3) Sequencing of the molecule (or clonal cluster of molecules) on a sequencer. E.g. the process of base-by-base resynthesis and sequencing on an Illumina sequencer _after_ cluster amplification. Errors in this phase are captured by the raw base quality scores from the sequencer.

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Instance Constructors

  1. new ConsensusCaller(errorRatePreLabeling: PhredScore, errorRatePostLabeling: PhredScore)

    errorRatePreLabeling

    an estimate of the error rate (i.e. rate of base substitutions) caused by DNA damage prior to any labeling of source molecules. Estimates the rate at which errors from Phase 1 described above would be observed if the rest of the process were error-free.

    errorRatePostLabeling

    an estimate of the error rate (i.e. rate of base substitutions) caused by DNA damage post-labeling. Estimates the errors from Phase 2 which would be non-uniform across replicates of the same source molecule.

Type Members

  1. class ConsensusBaseBuilder extends AnyRef

    An inner class for tracking the likelihoods for the consensus for a single base.

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 ConsensusCaller to any2stringadd[ConsensusCaller] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (ConsensusCaller, B)
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to ArrowAssoc[ConsensusCaller] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. def adjustedErrorProbability(qual: PhredScore): LogProbability

    Returns the adjusted probability of error given a base quality.

    Returns the adjusted probability of error given a base quality. This is the probability that the base was sequenced incorrectly or that the template had the wrong base due to an error during sample-preparation post-labeling (phase 2 described above).

    qual

    the raw base quality as a Phred scaled number

    returns

    the LogProbability that the base is incorrect

  7. def adjustedTruthProbability(qual: PhredScore): LogProbability

    Returns 1 - #adjustedErrorProbability

    Returns 1 - #adjustedErrorProbability

    qual

    the raw base quality as a Phred scaled number

    returns

    the LogProbability that the base is incorrect

  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def builder(): ConsensusBaseBuilder

    Returns a new builder that can be used to call the consensus at one or more sites serially.

  10. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
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    Annotations
    @throws( ... )
  11. def ensuring(cond: (ConsensusCaller) ⇒ Boolean, msg: ⇒ Any): ConsensusCaller
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to Ensuring[ConsensusCaller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: (ConsensusCaller) ⇒ Boolean): ConsensusCaller
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to Ensuring[ConsensusCaller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean, msg: ⇒ Any): ConsensusCaller
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to Ensuring[ConsensusCaller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: Boolean): ConsensusCaller
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to Ensuring[ConsensusCaller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to StringFormat[ConsensusCaller] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  19. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  20. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. final def notify(): Unit
    Definition Classes
    AnyRef
  24. final def notifyAll(): Unit
    Definition Classes
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  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  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): (ConsensusCaller, B)
    Implicit
    This member is added by an implicit conversion from ConsensusCaller to ArrowAssoc[ConsensusCaller] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

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