From ecebf0bc62effb0dcc76d12656e0919f8467a5a5 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Thu, 11 Feb 2010 18:39:26 +0000 Subject: [PATCH] Bug fix for null pointer exception in AnalyzeAnnotations if -name argument isn't specified git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2828 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/variantoptimizer/AnalyzeAnnotationsWalker.java | 2 -- .../walkers/variantoptimizer/AnnotationDataManager.java | 7 +++++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java index acbb2b10f..4b3c5f3de 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java @@ -68,8 +68,6 @@ public class AnalyzeAnnotationsWalker extends RodWalker { @Argument(fullName = "indicate_mean_num_vars", shortName = "meanNumVars", doc = "If supplied, plots will indicate the distribution of number of variants instead of distribution of value of annotation", required = false) private boolean INDICATE_MEAN_NUM_VARS = false; - - ///////////////////////////// // Private Member Variables ///////////////////////////// diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java index 80064ff67..d8c18db32 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java @@ -141,8 +141,11 @@ public class AnnotationDataManager { // Close the PrintStream output.close(); - - String annotationName = nameMap.get(annotationKey); + + String annotationName = null; + if( nameMap != null ) { + annotationName = nameMap.get(annotationKey); + } if( annotationName == null ) { // This annotation is not in the name map so use the key instead annotationName = annotationKey; }