From 29a3d9b47ae3e8550fd69edb98c2cf1e076c968d Mon Sep 17 00:00:00 2001 From: rpoplin Date: Tue, 29 Dec 2009 14:36:05 +0000 Subject: [PATCH] AnalyzeCovariates also has to skip over NO_DINUC git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2461 348d0f76-0448-11de-a6fe-93d51630548a --- .../analyzecovariates/AnalysisDataManager.java | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java index 58e12816b..23b2ca889 100755 --- a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java +++ b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java @@ -60,12 +60,15 @@ public class AnalysisDataManager { if( iii == 0 || !(qscore < IGNORE_QSCORES_LESS_THAN) ) { // use all data for the plot versus reported quality, but not for the other plots versus cycle and etc. newKey = new ArrayList(); newKey.add( key.get(0) ); // Make a new key with the read group ... - newKey.add( key.get(iii + 1) ); // and the given covariate - collapsedDatum = dataCollapsedByCovariate.get(iii).get( newKey ); - if( collapsedDatum == null ) { - dataCollapsedByCovariate.get(iii).put( newKey, new RecalDatum(fullDatum) ); - } else { - collapsedDatum.combine( fullDatum ); + Comparable theCovariateElement = key.get(iii + 1); // and the given covariate + if( theCovariateElement != null ) { + newKey.add( theCovariateElement ); + collapsedDatum = dataCollapsedByCovariate.get(iii).get( newKey ); + if( collapsedDatum == null ) { + dataCollapsedByCovariate.get(iii).put( newKey, new RecalDatum(fullDatum) ); + } else { + collapsedDatum.combine( fullDatum ); + } } } }