Added check in VariantContext.validate to ensure that getEnd() == END value when present

-- Fixed bug in VariantDataManager that this validation mode was intended to detect going forward
-- Still no VariantRecalibrationWalkersIntegrationTest for indels with BCF2 but that's because LowQual is missing from test VCF

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -298,7 +298,7 @@ public class VariantDataManager {
             attributes.put(VariantRecalibrator.VQS_LOD_KEY, String.format("%.4f", datum.lod));
             attributes.put(VariantRecalibrator.CULPRIT_KEY, (datum.worstAnnotation != -1 ? annotationKeys.get(datum.worstAnnotation) : "NULL"));
 
-            VariantContextBuilder builder = new VariantContextBuilder("VQSR", datum.loc.getContig(), datum.loc.getStart(), datum.loc.getStart(), alleles).attributes(attributes);
+            VariantContextBuilder builder = new VariantContextBuilder("VQSR", datum.loc.getContig(), datum.loc.getStart(), datum.loc.getStop(), alleles).attributes(attributes);
             recalWriter.add(builder.make());
         }
     }

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -1126,6 +1126,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
     // ---------------------------------------------------------------------------------------------------------
 
     private boolean validate(final EnumSet<Validation> validationToPerform) {
+        validateStop();
         for (final Validation val : validationToPerform ) {
             switch (val) {
                 case ALLELES: validateAlleles(); break;
@@ -1138,6 +1139,20 @@ public class VariantContext implements Feature { // to enable tribble integratio
         return true;
     }
 
+    /**
+     * Check that getEnd() == END from the info field, if it's present
+     */
+    private void validateStop() {
+        if ( hasAttribute(VCFConstants.END_KEY) ) {
+            final int end = getAttributeAsInt(VCFConstants.END_KEY, -1);
+            assert end != -1;
+            if ( end != getEnd() )
+                throw new ReviewedStingException("Badly formed variant context at location " + getChr() + ":"
+                        + getStart() + "; getEnd() was " + getEnd()
+                        + " but this VariantContext contains an END key with value " + end);
+        }
+    }
+
     private void validateReferencePadding() {
         if ( hasSymbolicAlleles() ) // symbolic alleles don't need padding...
             return;

public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -114,6 +114,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -tranchesFile " + getMd5DB().getMD5FilePath(params.tranchesMD5, null) +
                         " -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
                 Arrays.asList(params.cutVCFMD5));
+        spec.disableShadowBCF(); // has to be disabled because the input VCF is missing LowQual annotation
         executeTest("testApplyRecalibrationIndel-"+params.inVCF, spec);
     }