Packages

  • package root
    Definition Classes
    root
  • package com
    Definition Classes
    root
  • package fulcrumgenomics
    Definition Classes
    com
  • package umi
    Definition Classes
    fulcrumgenomics
  • 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.

    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.

    Definition Classes
    umi
  • ConsensusBaseBuilder

class ConsensusBaseBuilder extends AnyRef

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

Linear Supertypes
AnyRef, Any
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Inherited
  1. ConsensusBaseBuilder
  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

Instance Constructors

  1. new ConsensusBaseBuilder()

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

    Adds a base with adjusted error and truth probabilities to the consensus likelihoods.

  7. def add(base: Base, qual: PhredScore): Unit

    Adds a base and un-adjusted base quality to the consensus likelihoods.

  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def call(): (Base, PhredScore)

    Call the consensus base and quality score given the current set of likelihoods.

  10. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  11. def contributions: Int

    Returns the number of reads that contributed evidence to the consensus.

    Returns the number of reads that contributed evidence to the consensus. The value is equal to the number of times add() was called with non-ambiguous bases.

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

    Gives the calculated likelihoods of the four bases given the data and the model.

    Gives the calculated likelihoods of the four bases given the data and the model. The likelihoods returned factor in both the base observations and the probability of error prior to applying the labels.

  24. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  25. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  26. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  27. def observations(base: Base): Int

    Gets the number of observations of the base in question.

  28. def reset(): Unit

    Resets the likelihoods to p=1 so that the builder can be re-used.

  29. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  30. def toString(): String
    Definition Classes
    AnyRef → Any
  31. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  34. def →[B](y: B): (ConsensusBaseBuilder, B)
    Implicit
    This member is added by an implicit conversion from ConsensusBaseBuilder to ArrowAssoc[ConsensusBaseBuilder] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

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