From 3caa1b83bb220d1de1f7d5d3bc3b04b86f09c519 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Sat, 11 Feb 2012 11:48:32 -0500 Subject: [PATCH] Updating HC integration tests --- .../sting/gatk/walkers/bqsr/RecalDataManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java index a143ff98d..8a255391f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java @@ -181,7 +181,7 @@ public class RecalDataManager { } // Create dataCollapsedByCovariate's, the tables where everything except read group, quality score, and given covariate has been collapsed - for (int iii = 0; iii < dataCollapsedByCovariate.size(); iii++) { + for (int iii = 0; iii < dataCollapsedByCovariate.get(errorModel).size(); iii++) { covariateCollapsedKey[0] = key[0]; // Make a new key with the read group ... covariateCollapsedKey[1] = key[1]; // and quality score ... final Object theCovariateElement = key[iii + 2]; // and the given covariate