recalibration

Type Members

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

The algorithm proceeds in two phases.
The algorithm proceeds in two phases. First, we make a pass over the reads to collect statistics and build the recalibration tables. Then, we perform a second pass over the reads to apply the recalibration and assign adjusted quality scores.
trait Covariate extends AnyRef

A Covariate represents a predictor, also known as a "feature" or "independent variable".
A Covariate represents a predictor, also known as a "feature" or "independent variable".

Note
Concrete implementations of Covariate should inherit from AbstractCovariate, not Covariate.
class CovariateKey extends Serializable

Represents a tuple containing a value for each covariate.
Represents a tuple containing a value for each covariate.
The values for mandatory covariates are stored in member fields and optional covariate values are in extras.
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.
An empirical frequency count of mismatches from the reference.
This is used in ObservationTable, which maps from CovariateKey to Observation.
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

Value Members

object Aggregate extends Serializable
object BaseQualityRecalibration extends Serializable
object CovariateSpace extends Serializable
object Observation extends Serializable
object ObservationAccumulator extends Serializable
object RecalibrationTable extends Serializable
object Recalibrator extends Serializable

package recalibration

Type Members

abstract class AbstractCovariate[ValueT] extends Covariate with Serializable

class Aggregate extends Observation

class BaseQualityRecalibration extends Serializable with Logging

trait Covariate extends AnyRef

class CovariateKey extends Serializable

class CovariateSpace extends Serializable

class CycleCovariate extends AbstractCovariate[Int]

class DinucCovariate extends AbstractCovariate[(Char, Char)]

class ExtrasTables extends Serializable

class Observation extends Serializable

class ObservationAccumulator extends Serializable

class ObservationTable extends Serializable

class QualityTable extends Serializable

class RecalibrationTable extends (DecadentRead) ⇒ Seq[QualityScore] with Serializable

class Recalibrator extends Serializable

Value Members

object Aggregate extends Serializable

object BaseQualityRecalibration extends Serializable

object CovariateSpace extends Serializable

object Observation extends Serializable

object ObservationAccumulator extends Serializable

object RecalibrationTable extends Serializable

object Recalibrator extends Serializable

Ungrouped