From 96ea334bf2f351f8603ee2081eb640cc45e7142b Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 28 Jun 2012 15:27:44 -0400 Subject: [PATCH] Disable caching in BQSR for now since it significantly slows down computation; will look into this in a bit. --- .../sting/utils/recalibration/BaseRecalibration.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index 3612693da..785990315 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -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) 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) { recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base - qualityScoreByFullCovariateKey[errorModel.index].put(recalibratedQualityScore, keySet); + //qualityScoreByFullCovariateKey[errorModel.index].put(recalibratedQualityScore, wrappedKeySet); } quals[offset] = recalibratedQualityScore; }