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

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

@@ -165,6 +165,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     @Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping", required=false)
     private boolean requireStrictAlleleMatch = false;
 
+    @Argument(fullName="keepAC0", shortName="keepAC0", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
+    private boolean keepSitesWithAC0 = false;
+
     /**
      * If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
      * variant set, and evaluate the union of the results.  Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
@@ -580,4 +583,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     public GenomeAnalysisEngine getToolkit() {
         return super.getToolkit();
     }
+
+    public boolean ignoreAC0Sites() {
+        return ! keepSitesWithAC0;
+    }
 }

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

@@ -93,7 +93,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
         // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've
         // added in a proxy check for monomorphic status here.
         // Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call.
-       if ( vc1.isMonomorphicInSamples() ) {
+       if ( getWalker().ignoreAC0Sites() && vc1.isMonomorphicInSamples() ) {
             nRefLoci++;
         } else {
              switch (vc1.getType()) {

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

@@ -85,10 +85,13 @@ public class IndelLengthHistogram extends VariantEvaluator implements StandardEv
     @Override
     public void update1(final VariantContext eval, final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
         if ( eval.isIndel() && ! eval.isComplexIndel() ) {
-            for ( Allele alt : eval.getAlternateAlleles() ) {
-                final int alleleSize = alt.length() - eval.getReference().length();
-                if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
-                updateLengthHistogram(eval.getReference(), alt);
+            if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) {
+                // only if we are actually polymorphic in the subsetted samples should we count the allele
+                for ( Allele alt : eval.getAlternateAlleles() ) {
+                    final int alleleSize = alt.length() - eval.getReference().length();
+                    if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
+                    updateLengthHistogram(eval.getReference(), alt);
+                }
             }
         }
     }

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

@@ -134,7 +134,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
     @Override public int getComparisonOrder() { return 2; }
 
     public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( eval == null || eval.isMonomorphicInSamples() )
+        if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
             return;
 
         // update counts

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

@@ -92,7 +92,7 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
     @Override public int getComparisonOrder() { return 2; }
 
     public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( eval == null || eval.isMonomorphicInSamples() )
+        if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
             return;
 
         // update counts

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

@@ -33,7 +33,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
     }
 
     public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if (vc == null || !vc.isSNP() || !vc.hasGenotypes() || vc.isMonomorphicInSamples()) {
+        if (vc == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) {
             return;
         }
 

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

@@ -207,7 +207,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
     }
 
     public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( eval == null || eval.isMonomorphicInSamples() ) return;
+        if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
+            return;
 
         final Type type = getType(eval);
 

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

@@ -506,4 +506,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 UserException.class);
         executeTest("testIncompatibleEvalAndStrat", spec);
     }
+
+    public void testIncludingAC0(boolean includeAC0, final String md5) {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + testDir + "/ac0.vcf",
+                        "-L 20:81006 -noST -noEV -EV VariantSummary -o %s" + (includeAC0 ? " -keepAC0" : "")
+                ),
+                1,
+                Arrays.asList(md5));
+        executeTest("testIncludingAC0 keep ac 0 = " + includeAC0, spec);
+    }
+
+    @Test public void testWithAC0() { testIncludingAC0(true, "0ed2c8e4b4e06973a06838bc930a132d"); }
+    @Test public void testWithoutAC0() { testIncludingAC0(false, "79d28ddd0ab9584776b6cbefe48331df"); }
+
 }