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This caching in the BQSR seems to be too slow now that there are so many keys

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Ryan Poplin 2012-02-18 10:54:39 -05:00
parent 78718b8d6a
commit a8be96f63d
1 changed files with 6 additions and 5 deletions
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11
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -190,11 +190,12 @@ public class BaseRecalibration {
final Object[] fullCovariateKeyWithErrorMode = covariateKeySet.getKeySet(offset, errorModel); final Object[] fullCovariateKeyWithErrorMode = covariateKeySet.getKeySet(offset, errorModel);
final Object[] fullCovariateKey = Arrays.copyOfRange(fullCovariateKeyWithErrorMode, 0, fullCovariateKeyWithErrorMode.length-1); // need to strip off the error mode which was appended to the list of covariates final Object[] fullCovariateKey = Arrays.copyOfRange(fullCovariateKeyWithErrorMode, 0, fullCovariateKeyWithErrorMode.length-1); // need to strip off the error mode which was appended to the list of covariates
Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKeyWithErrorMode); // BUGBUG: This caching seems to put the entire key set into memory which negates the benefits of storing the delta delta tables?
if( qualityScore == null ) { //Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKeyWithErrorMode);
qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey ); //if( qualityScore == null ) {
qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKeyWithErrorMode); final byte qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey );
} // qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKeyWithErrorMode);
//}
recalQuals[offset] = qualityScore; recalQuals[offset] = qualityScore;
} }