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.

4. #### trait Covariate extends AnyRef

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

5. #### class CovariateKey extends Serializable

   Represents a tuple containing a value for each covariate.

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.

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