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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
This commit is contained in:
rpoplin 2010-02-03 20:33:15 +00:00
parent 280f38f635
commit 210c4c9913
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
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@ -62,6 +62,7 @@ public class AnnotationDataManager {
// Loop over each annotation in the vcf record // Loop over each annotation in the vcf record
final Map<String,String> infoField = variant.getInfoValues(); final Map<String,String> infoField = variant.getInfoValues();
infoField.put("QUAL", ((Double)variant.getQual()).toString() ); // add QUAL field to annotations
for( String annotationKey : infoField.keySet() ) { for( String annotationKey : infoField.keySet() ) {
float value; float value;
@ -151,7 +152,7 @@ public class AnnotationDataManager {
OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationName + " " + MIN_VARIANTS_PER_BIN + " " + INDICATE_MEAN_NUM_VARS; OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationName + " " + MIN_VARIANTS_PER_BIN + " " + INDICATE_MEAN_NUM_VARS;
System.out.println( rScriptCommandLine ); 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 { try {
Runtime.getRuntime().exec( rScriptCommandLine ); Runtime.getRuntime().exec( rScriptCommandLine );
} catch ( IOException e ) { } catch ( IOException e ) {