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fixup for BQSR (HC integration tests) 

In the new BQSR implementation, covariates do depend on the RecalibrationArgumentCollection.
This commit is contained in:
Mauricio Carneiro 2012-02-06 22:47:27 -05:00
parent 6e6f0f10e1
commit 5961868a7f
2 changed files with 4 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
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@ -87,6 +87,6 @@ public class RecalibrationArgumentCollection {
* The context covariate will use a context of this size to calculate it's covariate value * The context covariate will use a context of this size to calculate it's covariate value
*/ */
@Argument(fullName = "context_size", shortName = "cs", doc = "size of the k-mer context to be used", required = false) @Argument(fullName = "context_size", shortName = "cs", doc = "size of the k-mer context to be used", required = false)
int CONTEXT_SIZE = 8; public int CONTEXT_SIZE = 8;
} }

4
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.recalibration;
import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate; import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager; import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum; import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.collections.NestedHashMap;
@ -121,8 +122,9 @@ public class BaseRecalibration {
final boolean createCollapsedTables = true; final boolean createCollapsedTables = true;
// Initialize any covariate member variables using the shared argument collection // Initialize any covariate member variables using the shared argument collection
RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
for( Covariate cov : requestedCovariates ) { for( Covariate cov : requestedCovariates ) {
cov.initialize( null ); // BUGBUG: do any of the used covariates actually need the RecalibrationArgumentCollection? cov.initialize( RAC );
} }
// Initialize the data hashMaps // Initialize the data hashMaps
dataManager = new RecalDataManager( createCollapsedTables, requestedCovariates.size() ); dataManager = new RecalDataManager( createCollapsedTables, requestedCovariates.size() );