From b5ad5176f7d53228e9b36a5c059fe41d32da3943 Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 May 2009 20:35:50 +0000
Subject: [PATCH] stick headers on the output tables

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/PoolCaller.java     | 11 ++++++++++-
 .../gatk/walkers/SingleSampleGenotyper.java           |  6 +++++-
 .../playground/utils/AlleleFrequencyEstimate.java     |  2 +-
 3 files changed, 16 insertions(+), 3 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 a2001b845..559a7fe16 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
@@ -15,6 +15,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
+import java.util.zip.*;
 import java.io.*;
 
 // Draft iterative pooled caller
@@ -45,7 +46,8 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
 		try
 		{
 			discovery_output_file = new PrintStream(DISCOVERY_OUTPUT);
-			individual_output_file = new PrintStream(INDIVIDUAL_OUTPUT);
+			individual_output_file = new PrintStream(new GZIPOutputStream(new FileOutputStream(INDIVIDUAL_OUTPUT)));
+			individual_output_file.println(AlleleFrequencyEstimate.asTabularStringHeader());
 		} 
 		catch (Exception e)
 		{
@@ -324,6 +326,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
 
     public String reduceInit() 
     { 
+		discovery_output_file.printf("loc ref alt EM_alt_freq discovery_posterior discovery_null discovery_lod\n");
 		for (int i = 0; i < callers.size(); i++)
 		{
 			callers.get(i).reduceInit(); 
@@ -333,8 +336,14 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
 
     public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) 
     {
+		if (calls == null) { return ""; }
 		for (int i = 0; i < callers.size(); i++)
 		{
+			if (calls == null) { System.err.printf("calls == null\n"); }
+			if (calls[i] == null) { System.err.printf("calls[%d] == null\n", i); }
+			if (caller_sums == null) { System.err.printf("caller_sums == null\n"); }
+			if (callers.get(i) == null) { System.err.printf("callers[%d] == null\n", i); }
+			if (caller_sums.get(i) == null) { System.err.printf("caller_sums[%d] == null\n", i); }
 			caller_sums.set(i, callers.get(i).reduce(calls[i], caller_sums.get(i))); 
 		}
         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 761b7d1f0..1ba81fb24 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -49,7 +49,11 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 		{
 			sample_name = null; 
 			if (metricsFileName != null) { metrics    = new AlleleMetrics(metricsFileName, lodThreshold); }
-			if (callsFileName != null)   { calls_file = new PrintStream(callsFileName); }
+			if (callsFileName != null)   
+			{ 
+				calls_file = new PrintStream(callsFileName);  
+				calls_file.println(AlleleFrequencyEstimate.asTabularStringHeader());
+			}
 		}
 		catch (Exception e)
 		{
diff --git a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
index e07d8f8d8..3c86dedbb 100755
--- a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
@@ -147,7 +147,7 @@ public class AlleleFrequencyEstimate {
         return s;
     }
 
-    public String asTabularStringHeader() 
+    public static String asTabularStringHeader() 
 	{
 		return "location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases";
 	}