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Don't use asList because it maintains an iterator to the original list and then the result can't be used to create a new one

This commit is contained in:
Eric Banks 2012-06-11 15:45:58 -04:00
parent 41ef22fe7c
commit fea625632f
2 changed files with 4 additions and 3 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
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@ -364,8 +364,9 @@ public class RecalDataManager {
if (keyManager.getOptionalCovariates().size() > 0) { // initialize with the 'all covariates' table
// create a key manager for the delta table
List<Covariate> requiredCovariates = keyManager.getRequiredCovariates().subList(0, 1); // include the read group covariate as the only required covariate
List<Covariate> optionalCovariates = keyManager.getRequiredCovariates().subList(1, 2); // include the quality score covariate as an optional covariate
final List<Covariate> requiredCovariates = Arrays.asList(keyManager.getRequiredCovariates().get(0)); // include the read group covariate as the only required covariate
List<Covariate> optionalCovariates = new ArrayList<Covariate>();
optionalCovariates.add(keyManager.getRequiredCovariates().get(1)); // include the quality score covariate as an optional covariate
optionalCovariates.addAll(keyManager.getOptionalCovariates()); // include all optional covariates
deltaKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); // initialize the key manager
}

2
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -44,7 +44,7 @@ import java.util.*;
public class BaseRecalibration {
private QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done)
private LinkedHashMap<BQSRKeyManager, Map<BitSet, RecalDatum>> keysAndTablesMap; // quick access reference to the read group table and its key manager
private ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // list of all covariates to be used in this calculation
private ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // list of all covariates to be used in this calculation
/**