From a8be96f63dbc5545c516ada8acd96bf05b59904d Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Sat, 18 Feb 2012 10:54:39 -0500 Subject: [PATCH] This caching in the BQSR seems to be too slow now that there are so many keys --- .../sting/utils/recalibration/BaseRecalibration.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 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 4a366bc02..74083ced2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -190,11 +190,12 @@ public class BaseRecalibration { 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 - Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKeyWithErrorMode); - if( qualityScore == null ) { - qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey ); - qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKeyWithErrorMode); - } + // BUGBUG: This caching seems to put the entire key set into memory which negates the benefits of storing the delta delta tables? + //Byte qualityScore = (Byte) qualityScoreByFullCovariateKey.get(fullCovariateKeyWithErrorMode); + //if( qualityScore == null ) { + final byte qualityScore = performSequentialQualityCalculation( errorModel, fullCovariateKey ); + // qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKeyWithErrorMode); + //} recalQuals[offset] = qualityScore; }