org.broadinstitute.hellbender.utils.recalibration

Class RecalibrationTables

java.lang.Object

org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<NestedIntegerArray<RecalDatum>>

public final class RecalibrationTables
extends java.lang.Object
implements java.io.Serializable, java.lang.Iterable<NestedIntegerArray<RecalDatum>>

Utility class to facilitate base quality score recalibration.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
RecalibrationTables(StandardCovariateList covariates)
RecalibrationTables(StandardCovariateList covariates, int numReadGroups)

Method Summary

Modifier and Type	Method and Description
RecalibrationTables	combine(RecalibrationTables toMerge) Merge all of the tables from toMerge into into this set of tables
java.util.List<NestedIntegerArray<RecalDatum>>	getAdditionalTables()
Covariate	getCovariateForTable(NestedIntegerArray<RecalDatum> table)
NestedIntegerArray<RecalDatum>	getQualityScoreTable()
NestedIntegerArray<RecalDatum>	getReadGroupTable()
NestedIntegerArray<RecalDatum>	getTable(int index)
NestedIntegerArray<RecalDatum>	getTableForCovariate(Covariate cov)
static RecalibrationTables	inPlaceCombine(RecalibrationTables left, RecalibrationTables right) Combines the right table into the left table, in-place (without making a copy)
boolean	isAdditionalCovariateTable(NestedIntegerArray<RecalDatum> table)
boolean	isEmpty()
boolean	isQualityScoreTable(NestedIntegerArray<RecalDatum> table)
boolean	isReadGroupTable(NestedIntegerArray<RecalDatum> table)
java.util.Iterator<NestedIntegerArray<RecalDatum>>	iterator()
NestedIntegerArray<RecalDatum>	makeQualityScoreTable() Allocate a new quality score table, based on requested parameters in this set of tables, without any data in it.
int	numTables()
static RecalibrationTables	safeCombine(RecalibrationTables left, RecalibrationTables right) Combines the two tables into a new table (allocating a new table in the process)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

RecalibrationTables

public RecalibrationTables(StandardCovariateList covariates)

RecalibrationTables

public RecalibrationTables(StandardCovariateList covariates,
                           int numReadGroups)

Method Detail

getTableForCovariate

public NestedIntegerArray<RecalDatum> getTableForCovariate(Covariate cov)

getCovariateForTable

public Covariate getCovariateForTable(NestedIntegerArray<RecalDatum> table)

isReadGroupTable

public boolean isReadGroupTable(NestedIntegerArray<RecalDatum> table)

isQualityScoreTable

public boolean isQualityScoreTable(NestedIntegerArray<RecalDatum> table)

isAdditionalCovariateTable

public boolean isAdditionalCovariateTable(NestedIntegerArray<RecalDatum> table)

getReadGroupTable

public NestedIntegerArray<RecalDatum> getReadGroupTable()

getQualityScoreTable

public NestedIntegerArray<RecalDatum> getQualityScoreTable()

numTables

public int numTables()

iterator

public java.util.Iterator<NestedIntegerArray<RecalDatum>> iterator()

Specified by:

iterator in interface java.lang.Iterable<NestedIntegerArray<RecalDatum>>

isEmpty

public boolean isEmpty()

Returns:

true if all the tables contain no RecalDatums

makeQualityScoreTable

public NestedIntegerArray<RecalDatum> makeQualityScoreTable()

Allocate a new quality score table, based on requested parameters in this set of tables, without any data in it.

Returns:

a newly allocated, empty read group x quality score table

combine

public RecalibrationTables combine(RecalibrationTables toMerge)

Merge all of the tables from toMerge into into this set of tables

safeCombine

public static RecalibrationTables safeCombine(RecalibrationTables left,
                                              RecalibrationTables right)

Combines the two tables into a new table (allocating a new table in the process)

Parameters:

left - first table to combine

right - second table to combine

Returns:

a new table with the merged contents of left and right

inPlaceCombine

public static RecalibrationTables inPlaceCombine(RecalibrationTables left,
                                                 RecalibrationTables right)

Combines the right table into the left table, in-place (without making a copy)

Parameters:

left - first table to combine

right - second table to combine

Returns:

modified version of left with the contents of right incorporated into it

getTable

public NestedIntegerArray<RecalDatum> getTable(int index)

getAdditionalTables

public java.util.List<NestedIntegerArray<RecalDatum>> getAdditionalTables()