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
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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
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class
ConsensusBaseBuilder
extends AnyRef
An inner class for tracking the likelihoods for the consensus for a single base.
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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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
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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.
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final
def
==(arg0: Any): Boolean
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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
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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
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final
def
asInstanceOf[T0]: T0
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- Any
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def
builder(): ConsensusBaseBuilder
Returns a new builder that can be used to call the consensus at one or more sites serially.
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def
clone(): AnyRef
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- protected[java.lang]
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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
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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
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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
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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
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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def
equals(arg0: Any): Boolean
- Definition Classes
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def
finalize(): Unit
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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.
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- StringFormat
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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final
def
wait(arg0: Long): Unit
- Definition Classes
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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