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Disable caching in BQSR for now since it significantly slows down computation; will look into this in a bit.

This commit is contained in:
Eric Banks 2012-06-28 15:27:44 -04:00
parent e9d750297a
commit 96ea334bf2
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -112,10 +112,12 @@ public class BaseRecalibration {
if (originalQualityScore >= QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality) if (originalQualityScore >= QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality)
final int[] keySet = fullReadKeySet[offset]; // get the keyset for this base using the error model final int[] keySet = fullReadKeySet[offset]; // get the keyset for this base using the error model
Byte recalibratedQualityScore = (Byte) qualityScoreByFullCovariateKey[errorModel.index].get(wrapKeySet(keySet)); //final Object[] wrappedKeySet = wrapKeySet(keySet);
//Byte recalibratedQualityScore = (Byte) qualityScoreByFullCovariateKey[errorModel.index].get(wrappedKeySet);
Byte recalibratedQualityScore = null;
if (recalibratedQualityScore == null) { if (recalibratedQualityScore == null) {
recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base
qualityScoreByFullCovariateKey[errorModel.index].put(recalibratedQualityScore, keySet); //qualityScoreByFullCovariateKey[errorModel.index].put(recalibratedQualityScore, wrappedKeySet);
} }
quals[offset] = recalibratedQualityScore; quals[offset] = recalibratedQualityScore;
} }