Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -222,8 +222,33 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
             if ( isUniqueHeaderLine(line, hInfo) )
                 hInfo.add(line);
         }
-        for ( String expression : expressionsToUse )
+        // for the expressions, pull the info header line from the header of the resource rod
-            hInfo.add(new VCFInfoHeaderLine(expression, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"));
+        for ( VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions() ) {
+            // special case the ID field
+            if ( expression.fieldName.equals("ID") ) {
+                hInfo.add(new VCFInfoHeaderLine(expression.fullName, 1, VCFHeaderLineType.String, "ID field transferred from external VCF resource"));
+                continue;
+            }
+            VCFInfoHeaderLine targetHeaderLine = null;
+            for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
+                if ( line instanceof VCFInfoHeaderLine ) {
+                    VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
+                    if ( infoline.getName().equals(expression.fieldName) ) {
+                        targetHeaderLine = infoline;
+                        break;
+                    }
+                }
+            }
+
+            if ( targetHeaderLine != null ) {
+                if ( targetHeaderLine.getCountType() == VCFHeaderLineCount.INTEGER )
+                    hInfo.add(new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCount(), targetHeaderLine.getType(), targetHeaderLine.getDescription()));
+                else
+                    hInfo.add(new VCFInfoHeaderLine(expression.fullName, targetHeaderLine.getCountType(), targetHeaderLine.getType(), targetHeaderLine.getDescription()));
+            } else {
+                hInfo.add(new VCFInfoHeaderLine(expression.fullName, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"));
+            }
+        }
 
         engine.invokeAnnotationInitializationMethods(hInfo);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -49,20 +49,20 @@ public class VariantAnnotatorEngine {
     private AnnotatorCompatibleWalker walker;
     private GenomeAnalysisEngine toolkit;
 
-    private static class VAExpression {
+    protected static class VAExpression {
 
         public String fullName, fieldName;
         public RodBinding<VariantContext> binding;
 
-        public VAExpression(String fullEpression, List<RodBinding<VariantContext>> bindings) {
+        public VAExpression(String fullExpression, List<RodBinding<VariantContext>> bindings) {
-            int indexOfDot = fullEpression.lastIndexOf(".");
+            int indexOfDot = fullExpression.lastIndexOf(".");
             if ( indexOfDot == -1 )
-                throw new UserException.BadArgumentValue(fullEpression, "it should be in rodname.value format");
+                throw new UserException.BadArgumentValue(fullExpression, "it should be in rodname.value format");
 
-            fullName = fullEpression;
+            fullName = fullExpression;
-            fieldName = fullEpression.substring(indexOfDot+1);
+            fieldName = fullExpression.substring(indexOfDot+1);
 
-            String bindingName = fullEpression.substring(0, indexOfDot);
+            String bindingName = fullExpression.substring(0, indexOfDot);
             for ( RodBinding<VariantContext> rod : bindings ) {
                 if ( rod.getName().equals(bindingName) ) {
                     binding = rod;
@@ -97,6 +97,8 @@ public class VariantAnnotatorEngine {
             requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
     }
 
+    protected List<VAExpression> getRequestedExpressions() { return requestedExpressions; }
+
     private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude) {
         AnnotationInterfaceManager.validateAnnotations(annotationGroupsToUse, annotationsToUse);
         requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(annotationGroupsToUse, annotationsToUse);
@@ -211,8 +213,13 @@ public class VariantAnnotatorEngine {
                 continue;
 
             VariantContext vc = VCs.iterator().next();
-            if ( vc.hasAttribute(expression.fieldName) )
+            // special-case the ID field
+            if ( expression.fieldName.equals("ID") ) {
+                if ( vc.hasID() )
+                    infoAnnotations.put(expression.fullName, vc.getID());
+            } else if ( vc.hasAttribute(expression.fieldName) ) {
                 infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
+            }
         }
     }
 

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
-                Arrays.asList("4a6f0675242f685e9072c1da5ad9e715"));
+                Arrays.asList("1b4921085b26cbfe07d53b7c947de1e5"));
         executeTest("using expression with ID", spec);
     }