VariantEval can now see the EvaluationContext group objects, so they can decide if/when to print interesting sites. GenotypeConcordance has a hard-coded option to print FNs that is on the way to being generally useful. VCFWriter now uses the US locale for formatting floating point numbers; I believe this fixes a long-standing annoyance. Italian guys will check on this.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3864 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broad/tribble/vcf/VCFConstants.java

@@ -25,7 +25,10 @@
 
 package org.broad.tribble.vcf;
 
+import java.util.Locale;
+
 public final class VCFConstants {
+    public static final Locale VCF_LOCALE = Locale.US;
 
     // standard INFO/FORMAT field keys
     public static final String ANCESTRAL_ALLELE_KEY = "AA";

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

@@ -38,6 +38,8 @@ import java.util.*;
 
 @Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
 public class GenotypeConcordance extends VariantEvaluator {
+    private static final boolean  PRINT_INTERESTING_SITES = false;
+
     protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);
 
     // a mapping from allele count to stats
@@ -58,6 +60,7 @@ public class GenotypeConcordance extends VariantEvaluator {
 
     private static final int MAX_MISSED_VALIDATION_DATA = 100;
 
+    private VariantEvalWalker.EvaluationContext group = null;
 
     static class FrequencyStats implements TableType {
         class Stats {
@@ -229,7 +232,9 @@ public class GenotypeConcordance extends VariantEvaluator {
 
     private boolean warnedAboutValidationData = false;
 
-    public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
+        this.group = group;
+
         String interesting = null;
 
         // sanity check that we at least have either eval or validation data
@@ -287,7 +292,6 @@ public class GenotypeConcordance extends VariantEvaluator {
                     truth = Genotype.Type.NO_CALL;
                 } else {
                     truth = validation.getGenotype(sample).getType();
-                    // TODO -- capture "interesting" sites here, for example:
                     // interesting = "ConcordanceStatus=FP";
                 }
 
@@ -301,6 +305,9 @@ public class GenotypeConcordance extends VariantEvaluator {
             for (final String sample : validation.getSampleNames()) {
                 final Genotype.Type truth = validation.getGenotype(sample).getType();
                 sampleStats.incrValue(sample, truth, called);
+                if ( (truth == Genotype.Type.HOM_VAR || truth == Genotype.Type.HET) && called == Genotype.Type.NO_CALL ) {
+                    if ( PRINT_INTERESTING_SITES ) System.out.printf("%s: HM3 FN => %s%n", group, validation);
+                }
             }
         }
 

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

@@ -201,7 +201,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     // --------------------------------------------------------------------------------------------------------------
 
     /** private class holding all of the information about a single evaluation group (e.g., for eval ROD) */
-    private class EvaluationContext implements Comparable<EvaluationContext> {
+    public class EvaluationContext implements Comparable<EvaluationContext> {
         // useful for typing
         public String evalTrackName, compTrackName, novelty, filtered;
         public boolean enableInterestingSiteCaptures = false;
@@ -221,6 +221,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
             return Utils.join(CONTEXT_SEPARATOR, Arrays.asList(evalTrackName, compTrackName, selectExp == null ? "all" : selectExp.name, filtered, novelty));
         }
 
+        public String toString() { return getDisplayName(); }
+
         public int compareTo(EvaluationContext other) {
             return this.getDisplayName().compareTo(other.getDisplayName());
         }
@@ -495,7 +497,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                     switch ( evaluation.getComparisonOrder() ) {
                         case 1:
                             if ( evalWantsVC && vc != null ) {
-                                String interesting = evaluation.update1(vc, tracker, ref, context);
+                                String interesting = evaluation.update1(vc, tracker, ref, context, group);
                                 if ( interesting != null ) interestingReasons.add(interesting);
                             }
                             break;
@@ -506,7 +508,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                                     comp.hasNegLog10PError() &&
                                     comp.getNegLog10PError() < (minCompQualScore / 10.0) )
                                 comp = null;
-                            String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context );
+                            String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context, group );
                             if ( interesting != null ) interestingReasons.add(interesting);
                             break;
                         default:

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

@@ -59,10 +59,20 @@ abstract class VariantEvaluator {
         return null;
     }
 
+    public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
+        return update1(vc1, tracker, ref, context);
+    }
+
+
     public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         return null;
     }
 
+    public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
+        return update2(vc1, vc2, tracker, ref, context);
+    }
+
+
     /**
      * override this method for any finalization of calculations after the analysis is completed
      */

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java

@@ -239,7 +239,7 @@ public class VCFWriter {
     }
 
     private String getQualValue(double qual) {
-        String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
+        String s = String.format(VCFConstants.VCF_LOCALE, VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
         if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) )
             s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length());
         return s;
@@ -387,7 +387,7 @@ public class VCFWriter {
         if ( val == null )
             result = VCFConstants.MISSING_VALUE_v4;
         else if ( val instanceof Double )
-            result = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
+            result = String.format(VCFConstants.VCF_LOCALE, VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val);
         else if ( val instanceof Boolean )
             result = (Boolean)val ? "" : null; // empty string for true, null for false
         else if ( val instanceof List ) {