From 9902ce8073bbafb67bcb6a5d7f405ddfb839cfed Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 May 2009 13:57:58 +0000
Subject: [PATCH] properly flush the gzip output stream. this was a subtle
 inheritance bug.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/PoolCaller.java    | 18 +++++++++++++-----
 .../gatk/walkers/SingleSampleGenotyper.java    | 11 +++++++++++
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
index 559a7fe16..cc64fd3d7 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
@@ -315,12 +315,20 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
         return contexts;
     }
 
-    public void onTraversalDone() 
+    public void onTraversalDone(String result) 
     {
-		discovery_output_file.flush();
-		discovery_output_file.close();
-		individual_output_file.flush();
-		individual_output_file.close();
+		System.out.printf("OTD\n");
+		try 
+		{
+			discovery_output_file.flush();
+			discovery_output_file.close();
+			individual_output_file.flush();
+			individual_output_file.close();
+		}
+		catch (Exception e)
+		{
+			e.printStackTrace(); 
+		}
 		return;
     }
 
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 1ba81fb24..f3b87eb41 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -65,6 +65,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
     public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         String rodString = getRodString(tracker);
 
+		ref = Character.toUpperCase(ref);
 		if (ref == 'N') { return null; }
 
 		if (context.getReads().size() != 0)
@@ -252,6 +253,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 
         return bestAltBaseIndex;
     }
+
     private int[] getSecondaryBaseCounts(double[][] probs) {
         int[] secondaryBaseCounts = new int[4];
 
@@ -375,6 +377,15 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 		return "";
 	}
 
+	public void onTraversalDone()
+	{
+		if (callsFileName != null)   
+		{ 
+			calls_file.close();
+		}
+	}
+
+
 	/*
     public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) 
 	{