From 9ebcd6546d4253fa8baf5b6257226dff1225d39a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Jun 2009 17:07:38 +0000
Subject: [PATCH] Convenience printing

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@968 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../varianteval/HardyWeinbergEquilibrium.java    |  2 +-
 .../varianteval/PairwiseDistanceAnalysis.java    |  4 +++-
 .../walkers/varianteval/VariantDBCoverage.java   | 16 +++++-----------
 .../walkers/varianteval/VariantEvalWalker.java   |  2 ++
 4 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java
index 8e091ff0c..e459b4eb3 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java
@@ -79,7 +79,7 @@ public class HardyWeinbergEquilibrium extends BasicVariantAnalysis {
         List<String> s = new ArrayList<String>();
         s.add(String.format("n_calls              %d", nSites));
         s.add(String.format("n_violations         %d", nViolations));
-        s.add(String.format("violations_rate      %.2f", (100.0*nSites) / nViolations));
+        s.add(String.format("violations_rate      %.2f", (100.0*nViolations) / nSites));
         return s;
     }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PairwiseDistanceAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PairwiseDistanceAnalysis.java
index c5344775f..0090acb39 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PairwiseDistanceAnalysis.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PairwiseDistanceAnalysis.java
@@ -75,10 +75,12 @@ public class PairwiseDistanceAnalysis extends BasicVariantAnalysis {
 
         List<String> s = new ArrayList<String>();
         s.add(String.format("snps counted for pairwise distance: %d", pairWiseDistances.size()));
+        int cumulative = 0;
         for ( int i = 0; i < pairWiseBoundries.length; i++ ) {
             int maxDist = pairWiseBoundries[i];
             int count = pairCounts[i];
-            s.add(String.format("snps within %8d bp: %d", maxDist, count));
+            cumulative += count;
+            s.add(String.format("snps within %8d bp:    %d  %d", maxDist, count, cumulative));
         }
 
         return s;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
index 38bd7348e..d81a9e96d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
@@ -26,17 +26,10 @@ public class VariantDBCoverage extends BasicVariantAnalysis {
         if (inDB && inEval) nOverlapping++;
     }
 
-    public int nDBSites() {
-        return nDBObs;
-    }
-
-    public int nEvalSites() {
-        return nEvalObs;
-    }
-
-    public int nOverlappingSites() {
-        return nOverlapping;
-    }
+    public int nDBSites()           { return nDBObs; }
+    public int nEvalSites()         { return nEvalObs; }
+    public int nOverlappingSites()  { return nOverlapping; }
+    public int nNovelSites()        { return Math.abs(nEvalSites() - nOverlappingSites()); }
 
     /**
      * What fraction of the evaluated site variants were also found in the db?
@@ -70,6 +63,7 @@ public class VariantDBCoverage extends BasicVariantAnalysis {
         s.add(String.format("n_db_sites           %d", nDBSites()));
         s.add(String.format("n_eval_sites         %d", nEvalSites()));
         s.add(String.format("n_overlapping_sites  %d", nOverlappingSites()));
+        s.add(String.format("n_novel_sites        %d", nNovelSites()));
         s.add(String.format("per_eval_sites_in_db %.2f", 100*fractionEvalSitesCoveredByDB()));
         s.add(String.format("per_db_sites_in_eval %.2f", 100*fractionDBSitesDiscoveredInEval()));
         return s;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
index 2817d77b6..a59a7d8d2 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -103,6 +103,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         // Iterate over each analysis, and update it
         AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null);
+
+        //if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ);
         if ( eval != null && eval.getVariationConfidence() < minDiscoveryQ )
             eval = null;