Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -14,14 +14,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
-abstract class VariantEvaluator {
+public abstract class VariantEvaluator {
 //    protected boolean accumulateInterestingSites = false, printInterestingSites = false;
 //    protected String interestingSitePrefix = null;
-    protected boolean processedASite = false;
+//    protected boolean processedASite = false;
 //    protected List<VariantContext> interestingSites = new ArrayList<VariantContext>();
 
-    public abstract String getName();
-
 // do we want to keep track of things that are interesting
 //    public void accumulateInterestingSites(boolean enable)              { accumulateInterestingSites = enable; }
 //    public void printInterestingSites(String prefix)                    { printInterestingSites = true; interestingSitePrefix = prefix; }
@@ -35,6 +33,8 @@ abstract class VariantEvaluator {
 //            System.out.printf("%40s %s%n", interestingSitePrefix, why);
 //    }
 
+    public abstract String getName();
+
     protected VariantEvalWalker veWalker = null;
     public VariantEvaluator(VariantEvalWalker parent) {
         veWalker = parent;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java

@@ -1,16 +1,12 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval;
+package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
 
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 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.VariantEvaluatorBySample;
+import org.broadinstitute.sting.gatk.walkers.varianteval.*;
 import org.broadinstitute.sting.utils.report.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
-import org.broadinstitute.sting.utils.report.tags.Analysis;
-import org.broadinstitute.sting.utils.report.tags.DataPoint;
 
 import java.util.ArrayList;
 import java.util.List;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval;
+package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
 
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
@@ -6,10 +6,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.*;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
 import org.broadinstitute.sting.utils.report.tags.Analysis;
-import org.broadinstitute.sting.utils.report.tags.DataPoint;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -26,6 +24,7 @@ public class SimpleMetricsBySample extends VariantEvaluatorBySample {
         List<SampleDataPoint> points = new ArrayList(3);
         points.add(new CountSNPsSample());
         points.add(new TiTvRatioSample());
+        points.add(new HetHomRatioSample());
         points.add(new CompOverlapSample());
 
         return points;
@@ -92,6 +91,32 @@ class TiTvRatioSample extends SampleDataPoint {
     }
 }
 
+class HetHomRatioSample extends SampleDataPoint {
+    int nHet = 0;
+    int nHomVar = 0;
+
+    public HetHomRatioSample() {
+        super("HetHomRatio");
+    }
+
+    public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( vc != null ) {
+            Genotype g = vc.getGenotype(sampleName);
+            if ( g != null ) {
+                if ( g.isHet() ) {
+                    nHet++;
+                } else if (g.isHomVar()) {
+                    nHomVar++;
+                }
+            }
+        }
+    }
+
+    public String toString() {
+        return String.format("%.2f", ( ((double) nHet )/ nHomVar));
+    }
+}
+
 class CompOverlapSample extends SampleDataPoint {
     int nOverlap = 0;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java

@@ -1,10 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval;
+package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
 
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 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.*;
 import org.broadinstitute.sting.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.report.utils.TableType;