recalibration

abstract class AbstractCovariate[ValueT] extends Covariate with Serializable
class Aggregate extends Observation
class BaseQualityRecalibration extends Serializable with Logging

The algorithm proceeds in two phases.
trait Covariate extends AnyRef

A Covariate represents a predictor, also known as a "feature" or "independent variable".
class CovariateKey extends Serializable

Represents a tuple containing a value for each covariate.
class CovariateSpace extends Serializable

Represents the abstract space of all possible CovariateKeys for the given set of Covariates.
class CycleCovariate extends AbstractCovariate[Int]
class DinucCovariate extends AbstractCovariate[(Char, Char)]
class ExtrasTables extends Serializable
class Observation extends Serializable

An empirical frequency count of mismatches from the reference.
class ObservationAccumulator extends Serializable
class ObservationTable extends Serializable

Table containing the empirical frequency of mismatches for each set of covariate values.
class QualityTable extends Serializable
class RecalibrationTable extends (DecadentRead) ⇒ Seq[QualityScore] with Serializable
class Recalibrator extends Serializable