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