Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -83,6 +83,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     protected Boolean NO_STANDARD_MODULES = false;
 
     // Other arguments
+    @Argument(fullName="numSamples", shortName="ns", doc="Number of samples (used if no samples are available in the VCF file", required=false)
+    protected Integer NUM_SAMPLES = 0;
+
     @Argument(fullName="minPhaseQuality", shortName="mpq", doc="Minimum phasing quality", required=false)
     protected double MIN_PHASE_QUALITY = 10.0;
 
@@ -376,7 +379,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
         // Load the sample list
         sampleNamesForEvaluation.addAll(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
-        numSamples = sampleNamesForEvaluation.size();
+        numSamples = NUM_SAMPLES > 0 ? NUM_SAMPLES : sampleNamesForEvaluation.size();
 
         if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
             sampleNamesForStratification.addAll(sampleNamesForEvaluation);
@@ -507,7 +510,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
             if ( vc != null ) {
                 VariantContext vcsub = vc;
 
-                if (vc.hasGenotypes(sampleNamesForEvaluation)) {
+                if (vc.hasGenotypes() && vc.hasGenotypes(sampleNamesForEvaluation)) {
                     vcsub = getSubsetOfVariantContext(vc, sampleNamesForEvaluation);
                 }
 
@@ -516,7 +519,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                 }
 
                 // Now, if stratifying, split the subsetted vc per sample and add each as a new context
-                if ( trackPerSample ) {
+                if ( vc.hasGenotypes() && trackPerSample ) {
                     for ( String sampleName : sampleNamesForEvaluation ) {
                         VariantContext samplevc = getSubsetOfVariantContext(vc, sampleName);
     
@@ -669,7 +672,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
                     HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
                     for ( VariantStratifier vs : stratificationObjects ) {
-                        ArrayList<String> states = vs.getRelevantStates(ref, comp, compName, eval, sampleName);
+                        ArrayList<String> states = vs.getRelevantStates(ref, comp, compName, eval, evalName, sampleName);
                         stateMap.put(vs, states);
                     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java

@@ -123,8 +123,9 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
                 ac = Integer.valueOf(eval.getAttributeAsString("AC"));
             }
 
-            if ( ac != -1 )
+            if ( ac != -1 ) {
                 metrics.get(ac).update(eval);
+            }
         }
     }
 
@@ -150,19 +151,22 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
     }
 
     public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (numSamples == 0) {
+            return null;
+        }
+
         final String interesting = null;
 
-        if (eval != null ) {
+        if (eval != null) {
             if ( metrics == null ) {
                 int nSamples = numSamples;
 
-                if ( nSamples != -1 )
+                if ( nSamples != -1 ) {
                     metrics = new MetricsByAc(2 * nSamples);
+                }
             }
 
-            if ( eval.isSNP() &&
+            if ( eval.isSNP() && eval.isBiallelic() && metrics != null ) {
-                    eval.isBiallelic() &&
-                    metrics != null ) {
                 metrics.incrValue(eval);
             }
         }

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java

@@ -24,7 +24,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add(compName);

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java

@@ -22,7 +22,7 @@ public class CpG extends VariantStratifier implements StandardStratification {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         boolean isCpG = false;
         if (ref != null && ref.getBases() != null) {
             String fwRefBases = new String(ref.getBases());

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java

@@ -52,7 +52,7 @@ public class Degeneracy extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("all");

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java

@@ -17,17 +17,17 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
         this.evalNames = evalNames;
 
         states = new ArrayList<String>();
-        states.add("eval");
+        states.addAll(evalNames);
     }
 
     public ArrayList<String> getAllStates() {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
-        relevantStates.add("eval");
+        relevantStates.add(evalName);
 
         return relevantStates;
     }

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java

@@ -23,7 +23,7 @@ public class Filter extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("raw");

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java

@@ -24,7 +24,7 @@ public class FunctionalClass extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("all");

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java

@@ -27,7 +27,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
         relevantStates.add("none");
 

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

@@ -26,7 +26,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("all");

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java

@@ -22,7 +22,7 @@ public class Sample extends VariantStratifier {
         return samples;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
         relevantStates.add(sampleName);
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java

@@ -15,7 +15,7 @@ public abstract class VariantStratifier implements Comparable {
         return new ArrayList<String>();
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         return null;
     }
 

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

@@ -133,7 +133,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompVsEvalAC() {
         String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("113228ffa35e0f67b8e067860c04171f"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d8d59ec86ec9e00abad4ec44741de22f"));
         executeTestParallel("testCompVsEvalAC",spec);
         //executeTest("testCompVsEvalAC",spec);
     }
@@ -158,6 +158,36 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         //executeTest("testCompOverlap",spec);
     }
 
+    @Test
+    public void testEvalTrackWithoutGenotypes() {
+        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
+
+        String extraArgs = "-T VariantEval -R " +
+                           b37KGReference +
+                           " -L 20" +
+                           " -D " + dbsnp +
+                           " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                           " -noST -ST Novelty -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2e2c24b49f699506b967befbde5a6fa8"));
+        executeTestParallel("testEvalTrackWithoutGenotypes",spec);
+    }
+
+    @Test
+    public void testMultipleEvalTracksWithoutGenotypes() {
+        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
+
+        String extraArgs = "-T VariantEval -R " +
+                b37KGReference +
+                " -L 20" +
+                " -D " + dbsnp +
+                " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
+                " -noST -ST Novelty -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("144053b8bef5a79b23d0abd17b561294"));
+        executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
+    }
+
+
 //    @Test
 //    public void testVEValidatePass() {
 //        String extraArgs = "-L 1:1-10,000,000";