From 12dd18cdba1992c9a50aef9a7747df1fb20feac4 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 11 Jun 2009 21:15:34 +0000
Subject: [PATCH] Now aware of Hapmap and dbSNP sites.  We *can* change the
 priors there, but we don't yet.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@993 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/SingleSampleGenotyper.java   | 30 ++++++++++++++++---
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index c1eb7f35e..d1661f28e 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -80,11 +80,10 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 			}
 		}
 
-        AlleleFrequencyEstimate freq = getAlleleFrequency(ref, context, sample_name);
+        AlleleFrequencyEstimate freq = getAlleleFrequency(tracker, ref, context, sample_name);
 
         if (printMetrics) {
             if (freq != null) {
-                //System.out.println(context.getContig() + ":" + context.getPosition());
                 metrics.nextPosition(freq, tracker);
             }
             metrics.printMetricsAtLocusIntervals(metricsInterval);
@@ -93,7 +92,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
         return freq;
     }
 
-    private AlleleFrequencyEstimate getAlleleFrequency(char ref, LocusContext context, String sample_name) {
+    private AlleleFrequencyEstimate getAlleleFrequency(RefMetaDataTracker tracker, char ref, LocusContext context, String sample_name) {
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
         String bases = pileup.getBases();
 
@@ -123,7 +122,22 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
         
 		// Handle single-base polymorphisms.
         GenotypeLikelihoods G = new GenotypeLikelihoods(PRIOR_HOM_REF, PRIOR_HET, PRIOR_HOM_VAR);
-        for ( int i = 0; i < reads.size(); i++ )  
+
+        if (isHapmapSite(tracker)) {
+            //System.out.println(context.getLocation() + " is a Hapmap site.");
+
+            //G.setHomRefPrior(PRIOR_HOM_REF);
+            //G.setHetPrior(PRIOR_HET);
+            //G.setHomVarPrior(PRIOR_HOM_VAR);
+        } else if (isDbSNPSite(tracker)) {
+            //System.out.println(context.getLocation() + " is a dbSNP site.");
+
+            //G.setHomRefPrior(PRIOR_HOM_REF);
+            //G.setHetPrior(PRIOR_HET);
+            //G.setHomVarPrior(PRIOR_HOM_VAR);
+        }
+
+        for ( int i = 0; i < reads.size(); i++ )
         {
             SAMRecord read = reads.get(i);
             int offset = offsets.get(i);
@@ -139,6 +153,14 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
         return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name);
     }
 
+    private boolean isHapmapSite(RefMetaDataTracker tracker) {
+        return tracker.lookup("hapmap-chip", null) != null;
+    }
+
+    private boolean isDbSNPSite(RefMetaDataTracker tracker) {
+        return tracker.lookup("dbsnp", null) != null;
+    }
+
     private String getRodString(RefMetaDataTracker tracker) {
         String rodString = "";