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Updating to use the new VA interface 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3975 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-08 05:31:01 +00:00
parent bd6d5a8d51
commit 637a1e5055
2 changed files with 6 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -86,9 +86,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
String[] annotationsToUse = {};
String[] annotationClassesToUse = { "Standard" };
engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
ArrayList<String> annotationClassesToUse = new ArrayList<String>();
annotationClassesToUse.add("Standard");
engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, new ArrayList<String>());
if ( SET_KEY.toLowerCase().equals("null") )
SET_KEY = null;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
View File

@ -226,7 +226,9 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, Link
}
//instanciate the VariantAnnotatorEngine
engine = new VariantAnnotatorEngine(getToolkit(), new String[] { }, new String[] { "GenomicAnnotation" });
ArrayList<String> annotationsToUse = new ArrayList<String>();
annotationsToUse.add("GenomicAnnotation");
engine = new VariantAnnotatorEngine(getToolkit(), new ArrayList<String>(), annotationsToUse);
engine.setOneToMany( Boolean.TRUE.equals( ONE_TO_MANY ) );
engine.setRequestedColumns(SELECT_COLUMNS);
engine.setJoinTables(joinTables);