Bugfix for incorrect allele counting in IndelSummary

-- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs
-- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles
-- Update a few pieces of code to get previous correct behavior
-- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct)
-- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java

@@ -288,7 +288,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
     private VariantContext reduceVCToSamples(VariantContext vc, Set<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )
 //            logger.debug(String.format("  Sample %s has genotype %s, het = %s", sample, vc.getGenotype(sample), vc.getGenotype(sample).isHet() ));
-        VariantContext subvc = vc.subContextFromSamples(samplesToPhase, true);
+        VariantContext subvc = vc.subContextFromSamples(samplesToPhase);
 //        logger.debug("original VC = " + vc);
 //        logger.debug("sub      VC = " + subvc);
         return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF);

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java

@@ -43,7 +43,7 @@ public class GLBasedSampleSelector extends SampleSelector {
             return true;
         // want to include a site in the given samples if it is *likely* to be variant (via the EXACT model)
         // first subset to the samples
-        VariantContext subContext = vc.subContextFromSamples(samples, true);
+        VariantContext subContext = vc.subContextFromSamples(samples);
 
         // now check to see (using EXACT model) whether this should be variant
         // do we want to apply a prior? maybe user-spec?

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java

@@ -45,7 +45,7 @@ public class GTBasedSampleSelector extends SampleSelector{
         if ( samples == null || samples.isEmpty() )
             return true;
 
-        VariantContext subContext =  vc.subContextFromSamples(samples, false);
+        VariantContext subContext =  vc.subContextFromSamples(samples);
         if ( subContext.isPolymorphicInSamples() ) {
             return true;
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java

@@ -500,7 +500,10 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
 
     @Requires({"eval != null", "comp != null"})
     private EvalCompMatchType doEvalAndCompMatch(final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) {
-        // find all of the matching comps
+        if ( comp.getType() == VariantContext.Type.NO_VARIATION || eval.getType() == VariantContext.Type.NO_VARIATION )
+            // if either of these are NO_VARIATION they are LENIENT matches
+            return EvalCompMatchType.LENIENT;
+
         if ( comp.getType() != eval.getType() )
             return EvalCompMatchType.NO_MATCH;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java

@@ -57,9 +57,12 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv
         }
     }
 
-    public void update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if (vc1 != null) updateTiTv(vc1, false);
-        if (vc2 != null) updateTiTv(vc2, true);
+    @Override
+    public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (eval != null)
+            updateTiTv(eval, false);
+        if (comp != null)
+            updateTiTv(comp, true);
     }
 
     @Override

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java

@@ -28,7 +28,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
             final Collection<VariantContext> knownComps = tracker.getValues(knowns, ref.getLocus());
             for ( final VariantContext c : knownComps ) {
                 // loop over sites, looking for something that matches the type eval
-                if ( eval.getType() == c.getType() ) {
+                if ( eval.getType() == c.getType() || eval.getType() == VariantContext.Type.NO_VARIATION ) {
                     return KNOWN_STATES;
                 }
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java

@@ -197,7 +197,9 @@ public class VariantEvalUtils {
      * @return a new VariantContext with just the requested samples
      */
     public VariantContext getSubsetOfVariantContext(VariantContext vc, Set<String> sampleNames) {
-        return ensureAnnotations(vc, vc.subContextFromSamples(sampleNames, false));
+        // if we want to preserve AC0 sites as polymorphic we need to not rederive alleles
+        final boolean deriveAlleles = variantEvalWalker.ignoreAC0Sites();
+        return ensureAnnotations(vc, vc.subContextFromSamples(sampleNames, deriveAlleles));
     }
 
     public VariantContext ensureAnnotations(final VariantContext vc, final VariantContext vcsub) {
@@ -262,12 +264,8 @@ public class VariantEvalUtils {
                 // First, filter the VariantContext to represent only the samples for evaluation
                 VariantContext vcsub = vc;
 
-                if (subsetBySample && vc.hasGenotypes()) {
-                    if ( variantEvalWalker.isSubsettingToSpecificSamples() )
-                        vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
-                    else
-                        vcsub = ensureAnnotations(vc, vc);
-                }
+                if (subsetBySample && vc.hasGenotypes())
+                    vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
 
                 if ((byFilter || !vcsub.isFiltered())) {
                     addMapping(mapping, VariantEval.getAllSampleName(), vcsub);

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

@@ -334,12 +334,14 @@ public class VariantContext implements Feature { // to enable tribble integratio
      * in this VC is returned as the set of alleles in the subContext, even if
      * some of those alleles aren't in the samples
      *
+     * WARNING: BE CAREFUL WITH rederiveAllelesFromGenotypes UNLESS YOU KNOW WHAT YOU ARE DOING?
+     *
      * @param sampleNames    the sample names
-     * @param rederiveAllelesFromGenotypes if true, returns the alleles to just those in use by the samples
+     * @param rederiveAllelesFromGenotypes if true, returns the alleles to just those in use by the samples, true should be default
      * @return new VariantContext subsetting to just the given samples
      */
     public VariantContext subContextFromSamples(Set<String> sampleNames, final boolean rederiveAllelesFromGenotypes ) {
-        if ( sampleNames.containsAll(getSampleNames()) ) {
+        if ( sampleNames.containsAll(getSampleNames()) && ! rederiveAllelesFromGenotypes ) {
             return this; // fast path when you don't have any work to do
         } else {
             VariantContextBuilder builder = new VariantContextBuilder(this);
@@ -355,8 +357,18 @@ public class VariantContext implements Feature { // to enable tribble integratio
         }
     }
 
+    /**
+     * @see #subContextFromSamples(java.util.Set, boolean) with rederiveAllelesFromGenotypes = true
+     *
+     * @param sampleNames
+     * @return
+     */
+    public VariantContext subContextFromSamples(final Set<String> sampleNames) {
+        return subContextFromSamples(sampleNames, true);
+    }
+
     public VariantContext subContextFromSample(String sampleName) {
-        return subContextFromSamples(Collections.singleton(sampleName), true);
+        return subContextFromSamples(Collections.singleton(sampleName));
     }
 
     /**

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -34,7 +34,7 @@ import java.util.Arrays;
 import java.util.List;
 
 public class VariantEvalIntegrationTest extends WalkerTest {
-    private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval/";
+    private static String variantEvalTestDataRoot = privateTestDir + "VariantEval/";
     private static String fundamentalTestVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
     private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.vcf";
     private static String fundamentalTestSNPsWithMLEVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.withMLE.vcf";
@@ -122,7 +122,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("e62a3bd9914d48e2bb2fb4f5dfc5ebc0")
+                Arrays.asList("40abbc9be663aed8ee1158f832463ca8")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
     }
@@ -144,7 +144,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("087a2d9943c53e7f49663667c3305c7e")
+                Arrays.asList("106a0e8753e839c0a2c030eb4b165fa9")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
     }

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java

@@ -152,7 +152,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
                     public void run(final VariantContext vc) {
                         if ( samples == null )
                             samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
-                        VariantContext sub = vc.subContextFromSamples(samples, true);
+                        VariantContext sub = vc.subContextFromSamples(samples);
                         sub.getNSamples();
                     }
                 };