Removing update0 support in VariantEval

-- Now the only use for update0, calculating the number of processed loci, is centrally tracked in the walker itself not the evaluations.
-- This allows us to avoid calling update0 are every genomic base in 100ks of evaluates when there are a lot of stratifications.
-- No need to modify the integration tests, this optimization doesn't change the result of the calculation

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

@@ -214,6 +214,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     // Public constants
     private static String ALL_SAMPLE_NAME = "all";
 
+    // the number of processed bp for this walker
+    long nProcessedLoci = 0;
+
     // Utility class
     private final VariantEvalUtils variantEvalUtils = new VariantEvalUtils(this);
 
@@ -326,10 +329,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
      */
     @Override
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        for ( final NewEvaluationContext nec : evaluationContexts.values() ) {
+        // we track the processed bp and expose this for modules instead of wasting CPU power on calculating
-            synchronized (nec) {
+        // the same thing over and over in evals that want the processed bp
-                nec.update0(tracker, ref, context);
+        synchronized (this) {
-            }
+            nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
         }
 
         if (tracker != null) {
@@ -455,7 +458,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                     if ( lenientMatch == null ) lenientMatch = comp;
                     break;
                 case NO_MATCH:
-                    ;
+                    // do nothing
             }
         }
 
@@ -581,6 +584,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
     public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }
 
+    public long getnProcessedLoci() {
+        return nProcessedLoci;
+    }
+
     public Set<String> getContigNames() {
         final TreeSet<String> contigs = new TreeSet<String>();
         for( final SAMSequenceRecord r :  getToolkit().getReferenceDataSource().getReference().getSequenceDictionary().getSequences()) {

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

@@ -89,10 +89,6 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
         return 1;   // we only need to see each eval track
     }
 
-    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
-    }
-
     public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         nCalledLoci++;
 
@@ -192,6 +188,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     }
 
     public void finalizeEvaluation() {
+        nProcessedLoci = getWalker().getnProcessedLoci();
         variantRate = perLocusRate(nVariantLoci);
         variantRatePerBp = perLocusRInverseRate(nVariantLoci);
         heterozygosity = perLocusRate(nHets);

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

@@ -60,6 +60,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
     double minPhaseQuality = 10.0;
 
     public void initialize(VariantEvalWalker walker) {
+        super.initialize(walker);
         this.samplePhasingStatistics = new SamplePhasingStatistics(walker.getMinPhaseQuality());
         this.samplePrevGenotypes = new SamplePreviousGenotypes();
     }
@@ -294,14 +295,6 @@ class CompEvalGenotypes {
     public Genotype getEvalGenotype() {
         return evalGt;
     }
-
-    public void setCompGenotype(Genotype compGt) {
-        this.compGt = compGt;
-    }
-
-    public void setEvalGenotype(Genotype evalGt) {
-        this.evalGt = evalGt;
-    }
 }
 
 class SamplePreviousGenotypes {

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

@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.PrintStream;
 import java.util.Map;
 import java.util.Set;
 
@@ -60,17 +59,6 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
     @DataPoint(description = "Number of mendelian violations found", format = "%d")
     long nViolations;
 
-
-    /*@DataPoint(description = "number of child hom ref calls where the parent was hom variant", format = "%d")
-    long KidHomRef_ParentHomVar;
-    @DataPoint(description = "number of child het calls where the parent was hom ref", format = "%d")
-    long KidHet_ParentsHomRef;
-    @DataPoint(description = "number of child het calls where the parent was hom variant", format = "%d")
-    long KidHet_ParentsHomVar;
-    @DataPoint(description = "number of child hom variant calls where the parent was hom ref", format = "%d")
-    long KidHomVar_ParentHomRef;
-    */
-
     @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HOM_VAR", format = "%d")
     long mvRefRef_Var;
     @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HET", format = "%d")
@@ -88,12 +76,6 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
     @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HET", format = "%d")
     long mvVarVar_Het;
 
-
-    /*@DataPoint(description ="Number of inherited var alleles from het parents", format = "%d")
-    long nInheritedVar;
-    @DataPoint(description ="Number of inherited ref alleles from het parents", format = "%d")
-    long nInheritedRef;*/
-
     @DataPoint(description="Number of HomRef/HomRef/HomRef trios", format = "%d")
     long HomRefHomRef_HomRef;
     @DataPoint(description="Number of Het/Het/Het trios", format = "%d")
@@ -120,18 +102,15 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
     long HomVarHet_inheritedVar;
 
     MendelianViolation mv;
-    PrintStream mvFile;
     Map<String,Set<Sample>> families;
 
     public void initialize(VariantEvalWalker walker) {
-        //Changed by Laurent Francioli - 2011-06-07
+        super.initialize(walker);
-        //mv = new MendelianViolation(walker.getFamilyStructure(), walker.getMendelianViolationQualThreshold());
         mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false);
         families = walker.getSampleDB().getFamilies();
     }
 
     public boolean enabled() {
-        //return getVEWalker().FAMILY_STRUCTURE != null;
         return true;
     }
 

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

@@ -28,11 +28,12 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 @Analysis(description = "Evaluation summary for multi-allelic variants")
 public class MultiallelicSummary extends VariantEvaluator implements StandardEval {
@@ -90,10 +91,6 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
     @Override public boolean enabled() { return true; }
     @Override public int getComparisonOrder() { return 2; }
 
-    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
-    }
-
     public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( eval == null || eval.isMonomorphicInSamples() )
             return null;
@@ -152,6 +149,7 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
     }
 
     public void finalizeEvaluation() {
+        nProcessedLoci = getWalker().getnProcessedLoci();
         processedMultiSnpRatio = (double)nMultiSNPs / (double)nProcessedLoci;
         variantMultiSnpRatio = (double)nMultiSNPs / (double)nSNPs;
         processedMultiIndelRatio = (double)nMultiIndels / (double)nProcessedLoci;

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

@@ -4,14 +4,18 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Collection;
-
 public abstract class VariantEvaluator {
-    public void initialize(VariantEvalWalker walker) {}
+    private VariantEvalWalker walker;
+
+    public void initialize(VariantEvalWalker walker) {
+        this.walker = walker;
+    }
+
+    public VariantEvalWalker getWalker() {
+        return walker;
+    }
 
     public abstract boolean enabled();
 
@@ -19,9 +23,8 @@ public abstract class VariantEvaluator {
     public abstract int getComparisonOrder();
 
     // called at all sites, regardless of eval context itself; useful for counting processed bases
-    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    // No longer available.  The processed bp is kept in VEW itself for performance reasons
-
+    //    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-    }
 
     public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         return null;
@@ -45,17 +48,13 @@ public abstract class VariantEvaluator {
         return ((double)num) / (Math.max(denom, 1));
     }
 
-    public boolean stateIsApplicable(StateKey stateKey) {
-        return true;
-    }
-
     /**
      * Returns true if the variant in vc was a singleton in the original input evaluation
      * set, regardless of variant context subsetting that has occurred.
-     * @param eval
+     * @param eval the VariantContext being assessed for this previous status as a singleton
      * @return true if eval was originally a singleton site
      */
-    protected static final boolean variantWasSingleton(final VariantContext eval) {
+    protected static boolean variantWasSingleton(final VariantContext eval) {
         return eval.getAttributeAsBoolean(VariantEvalWalker.IS_SINGLETON_KEY, false);
     }
 
@@ -66,7 +65,7 @@ public abstract class VariantEvaluator {
      * @param all number of all variants
      * @return a String novelty rate, or NA if all == 0
      */
-    protected static final String formattedNoveltyRate(final int known, final int all) {
+    protected static String formattedNoveltyRate(final int known, final int all) {
         return formattedPercent(all - known, all);
     }
 
@@ -77,7 +76,7 @@ public abstract class VariantEvaluator {
      * @param total count of all objects, including x
      * @return a String percent rate, or NA if total == 0
      */
-    protected static final String formattedPercent(final int x, final int total) {
+    protected static String formattedPercent(final int x, final int total) {
         return total == 0 ? "NA" : String.format("%.2f", x / (1.0*total));
     }
 
@@ -88,7 +87,7 @@ public abstract class VariantEvaluator {
      * @param denom number of observations in the denumerator
      * @return a String formatted ratio, or NA if all == 0
      */
-    protected static final String formattedRatio(final int num, final int denom) {
+    protected static String formattedRatio(final int num, final int denom) {
         return denom == 0 ? "NA" : String.format("%.2f", num / (1.0 * denom));
     }
 }

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

@@ -49,7 +49,6 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
     /** Indels with size greater than this value are tallied in the CNV column */
     private final static int MAX_INDEL_LENGTH = 50;
     private final static double MIN_CNV_OVERLAP = 0.5;
-    private VariantEvalWalker walker;
 
     public enum Type {
         SNP, INDEL, CNV
@@ -152,7 +151,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
 
 
     public void initialize(VariantEvalWalker walker) {
-        this.walker = walker;
+        super.initialize(walker);
 
         nSamples = walker.getSampleNamesForEvaluation().size();
         countsPerSample = new TypeSampleMap(walker.getSampleNamesForEvaluation());
@@ -176,11 +175,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
         return 2;   // we only need to see each eval track
     }
 
-    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    private Type getType(VariantContext vc) {
-        nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
-    }
-
-    private final Type getType(VariantContext vc) {
         switch (vc.getType()) {
             case SNP:
                 return Type.SNP;
@@ -196,9 +191,9 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
         }
     }
 
-    private final boolean overlapsKnownCNV(VariantContext cnv) {
+    private boolean overlapsKnownCNV(VariantContext cnv) {
         if ( knownCNVs != null ) {
-            final GenomeLoc loc = walker.getGenomeLocParser().createGenomeLoc(cnv, true);
+            final GenomeLoc loc = getWalker().getGenomeLocParser().createGenomeLoc(cnv, true);
             IntervalTree<GenomeLoc> intervalTree = knownCNVs.get(loc.getContig());
 
             final Iterator<IntervalTree.Node<GenomeLoc>> nodeIt = intervalTree.overlappers(loc.getStart(), loc.getStop());
@@ -252,13 +247,14 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
         return null; // we don't capture any interesting sites
     }
 
-    private final String noveltyRate(Type type) {
+    private String noveltyRate(Type type) {
         final int all = allVariantCounts.all(type);
         final int known = knownVariantCounts.all(type);
         return formattedNoveltyRate(known, all);
     }
 
     public void finalizeEvaluation() {
+        nProcessedLoci = getWalker().getnProcessedLoci();
         nSNPs = allVariantCounts.all(Type.SNP);
         nIndels = allVariantCounts.all(Type.INDEL);
         nSVs = allVariantCounts.all(Type.CNV);

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

@@ -23,9 +23,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
                 final VariantEvaluator eval = c.newInstance();
                 eval.initialize(walker);
 
-                if (eval.stateIsApplicable(stateKey)) {
+                evaluationInstances.put(c.getSimpleName(), eval);
-                    evaluationInstances.put(c.getSimpleName(), eval);
-                }
             } catch (InstantiationException e) {
                 throw new StingException("Unable to instantiate eval module '" + c.getSimpleName() + "'");
             } catch (IllegalAccessException e) {
@@ -40,8 +38,6 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
 
     public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
         for ( final VariantEvaluator evaluation : evaluationInstances.values() ) {
-            // we always call update0 in case the evaluation tracks things like number of bases covered
-
             // the other updateN methods don't see a null context
             if ( tracker == null )
                 continue;
@@ -65,10 +61,4 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
             }
         }
     }
-
-    public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        for ( final VariantEvaluator evaluation : evaluationInstances.values() ) {
-            evaluation.update0(tracker, ref, context);
-        }
-    }
 }