From 210c4c99130837aac3b2cc0f3c06b6ca1eba7791 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Wed, 3 Feb 2010 20:33:15 +0000 Subject: [PATCH] AnalyzeAnnotations now makes plots for the value in the QUAL column as if it were an annotation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2771 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variantoptimizer/AnnotationDataManager.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 d61d6a65d..80064ff67 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 @@ -62,6 +62,7 @@ public class AnnotationDataManager { // Loop over each annotation in the vcf record final Map infoField = variant.getInfoValues(); + infoField.put("QUAL", ((Double)variant.getQual()).toString() ); // add QUAL field to annotations for( String annotationKey : infoField.keySet() ) { float value; @@ -151,7 +152,7 @@ public class AnnotationDataManager { OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationName + " " + MIN_VARIANTS_PER_BIN + " " + INDICATE_MEAN_NUM_VARS; System.out.println( rScriptCommandLine ); - // Execute the RScript command to plot the table of TiTv values + // Execute the RScript command to plot the table of truth values try { Runtime.getRuntime().exec( rScriptCommandLine ); } catch ( IOException e ) {