From 54355b186426d3bd70ddd84098604b1fe3d524fc Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Aug 2010 19:07:59 +0000
Subject: [PATCH] In variant quality score recalibrator Preserve the definition
 of known and novel to be presence in dbSNP or not even when training with 1KG
 project calls.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4151 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../GenerateVariantClustersWalker.java                     | 7 ++-----
 .../walkers/variantrecalibration/VariantRecalibrator.java  | 5 +----
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 5e0ece02a..3f9af10d8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -181,22 +181,19 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
                     variantDatum.annotations = annotationValues;
                     variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
 
-                    variantDatum.isKnown = false;
-                    variantDatum.weight = WEIGHT_NOVELS;
                     variantDatum.qual = vc.getPhredScaledQual();
 
                     final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
                     final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
                     final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
 
+                    variantDatum.isKnown = (dbsnp!=null);
+                    variantDatum.weight = WEIGHT_NOVELS;                   
                     if( vcHapMap != null ) {
-                        variantDatum.isKnown = true;
                         variantDatum.weight = WEIGHT_HAPMAP;
                     } else if( vc1KG != null ) {
-                        variantDatum.isKnown = true;
                         variantDatum.weight = WEIGHT_1KG;
                     } else if( dbsnp != null ) {
-                        variantDatum.isKnown = true;
                         variantDatum.weight = WEIGHT_DBSNP;
                     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 2573bb6e1..b2e770ca7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -214,16 +214,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
                     final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
 
-                    variantDatum.isKnown = false;
+                    variantDatum.isKnown = (dbsnp!=null);
                     double knownPrior_qScore = PRIOR_NOVELS;
                     if( vcHapMap != null ) {
-                        variantDatum.isKnown = true;
                         knownPrior_qScore = PRIOR_HAPMAP;
                     } else if( vc1KG != null ) {
-                        variantDatum.isKnown = true;
                         knownPrior_qScore = PRIOR_1KG;
                     } else if( dbsnp != null ) {
-                        variantDatum.isKnown = true;
                         knownPrior_qScore = PRIOR_DBSNP;
                     }
                     final double knownPrior = QualityUtils.qualToProb(knownPrior_qScore);