Fixed issue where comp tracks with genotypes that didn't exactly overlap the eval track were getting dropped. Fixed issue where the 'row' column wasn't being output for things implementing TableType. This is an urgent patch for Mark - it'll break tests until I go back and update the md5s.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5374 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -285,6 +285,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                                     table.addColumn(columnName, "unknown");
                                 }
 
+                                table.addColumn("row", "unknown");
+
                                 for ( Object o : t.getColumnKeys() ) {
                                     String c;
 
@@ -319,6 +321,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
                                     String newStateKey = stateKey.toString() + r;
                                     table.set(newStateKey, c, t.getCell(row, col));
+
+                                    table.set(newStateKey, "row", r);
                                 }
                             }
                         } else {

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

@@ -85,7 +85,7 @@ public class GenotypeConcordance extends VariantEvaluator {
         public Object[] getRowKeys() {
             String rows[] = new String[foundMissedByAC.size()];
             int index = 0;
-            for (int i : foundMissedByAC.keySet()) rows[index++] = "Allele Count " + i;
+            for (int i : foundMissedByAC.keySet()) rows[index++] = "AlleleCount_" + i;
             return rows;
         }
 
@@ -471,11 +471,11 @@ class SampleStats implements TableType {
 //                            "n_het/ref","n_het/het","n_het/hom",
 //                            "total_true_hom","%_hom/hom","n_hom/no-call",
 //                            "n_hom/ref","n_hom/het","n_hom/hom"};
-        return new String[]{"total_true_ref","pct_ref_vs_ref","n_ref_vs_no-call",
+        return new String[]{"total_true_ref","pct_ref_vs_ref","n_ref_vs_no_call",
                 "n_ref_vs_ref","n_ref_vs_het","n_ref_vs_hom",
-                "total_true_het","pct_het_vs_het","n_het_vs_no-call",
+                "total_true_het","pct_het_vs_het","n_het_vs_no_call",
                 "n_het_vs_ref","n_het_vs_het","n_het_vs_hom",
-                "total_true_hom","pct_hom_vs_hom","n_hom_vs_no-call",
+                "total_true_hom","pct_hom_vs_hom","n_hom_vs_no_call",
                 "n_hom_vs_ref","n_hom_vs_het","n_hom_vs_hom"};
     }
 
@@ -560,9 +560,9 @@ class SampleSummaryStats implements TableType {
             "percent_comp_het_called_var",
             "percent_comp_hom_called_hom",
             "percent_comp_hom_called_var",
-            "percent_non-reference_sensitivity",
+            "percent_non_reference_sensitivity",
             "percent_overall_genotype_concordance",
-            "percent_non-reference_discrepancy_rate"};
+            "percent_non_reference_discrepancy_rate"};
 
     // sample to concordance stats object
     protected final HashMap<String, double[]> concordanceSummary = new HashMap<String, double[]>();

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

@@ -342,12 +342,13 @@ public class VariantEvalUtils {
      * @param allowableTypes a set of allowable variation types
      * @param byFilter       if false, only accept PASSing VariantContexts.  Otherwise, accept both PASSing and filtered
      *                       sites
+     * @param subsetBySample if false, do not separate the track into per-sample VCs
      * @param trackPerSample if false, don't stratify per sample (and don't cut up the VariantContext like we would need
      *                       to do this)
      * @param allowNoCalls   if false, don't accept no-call loci from a variant track
      * @return a mapping of track names to a list of VariantContext objects
      */
-    public HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean trackPerSample, boolean allowNoCalls) {
+    public HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean subsetBySample, boolean trackPerSample, boolean allowNoCalls) {
         HashMap<String, HashMap<String, VariantContext>> bindings = new HashMap<String, HashMap<String, VariantContext>>();
 
         for (String trackName : trackNames) {
@@ -360,7 +361,7 @@ public class VariantEvalUtils {
             if (vc != null) {
                 VariantContext vcsub = vc;
 
-                if (vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation())) {
+                if (subsetBySample && vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation())) {
                     vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
                 }
 
@@ -411,8 +412,8 @@ public class VariantEvalUtils {
             }
         }
 
-        HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, perSampleIsEnabled, true);
+        HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, true, perSampleIsEnabled, true);
-        HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false);
+        HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false, false);
 
         vcs.putAll(compBindings);
         vcs.putAll(evalBindings);