org.bdgenomics.adam.rdd.read

recalibration

package recalibration

Visibility
  1. Public
  2. All

Type Members

  1. abstract class AbstractCovariate[ValueT] extends Covariate with Serializable

  2. class Aggregate extends Observation

  3. 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.

  4. 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.

  5. 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.

  6. class CovariateSpace extends Serializable

    Represents the abstract space of all possible CovariateKeys for the given set of Covariates.

  7. class CycleCovariate extends AbstractCovariate[Int]

  8. class DinucCovariate extends AbstractCovariate[(Char, Char)]

  9. class ExtrasTables extends Serializable

  10. 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.

  11. class ObservationAccumulator extends Serializable

  12. class ObservationTable extends Serializable

    Table containing the empirical frequency of mismatches for each set of covariate values.

  13. class QualityTable extends Serializable

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

  15. class Recalibrator extends Serializable

Value Members

  1. object Aggregate extends Serializable

  2. object BaseQualityRecalibration extends Serializable

  3. object CovariateSpace extends Serializable

  4. object Observation extends Serializable

  5. object ObservationAccumulator extends Serializable

  6. object RecalibrationTable extends Serializable

  7. object Recalibrator extends Serializable

Ungrouped