From 2cd9a1597f25d384898ca53c412f267745ddee2e Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 14:09:14 +0000
Subject: [PATCH] Simple improvements to allele caller

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@254 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/AlleleFrequencyWalker.java   | 20 ++++++++++++++++---
 .../utils/AlleleFrequencyEstimate.java        |  2 ++
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index c0504b6a4..7af695b56 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.*;
+import org.apache.log4j.Logger;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
@@ -18,7 +19,11 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
 {
     @Argument public int    N;
     @Argument public int    DOWNSAMPLE;
-    @Argument public String GFF_OUTPUT_FILE;
+    @Argument(required=false,defaultValue="")
+    public String GFF_OUTPUT_FILE;
+
+
+    protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
 
     Random random;
     PrintStream output;
@@ -29,6 +34,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         String bases = getBases(context);
         double quals[][] = getOneBaseQuals(context);
 
+        logger.debug(String.format("In alleleFrequnecy walker: N=%d, d=%d", N, DOWNSAMPLE));
+
         if ((DOWNSAMPLE != 0) && (DOWNSAMPLE < bases.length()))
         {
             String downsampled_bases     = "";
@@ -88,6 +95,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
                 }
             }
         }
+
+        logger.debug(String.format(" => result is %s", alleleFreq));
+
         return alleleFreq;
     }
 
@@ -447,7 +457,10 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
             this.random = new java.util.Random(0);
-            this.output = new PrintStream(GFF_OUTPUT_FILE);
+            if ( GFF_OUTPUT_FILE == null )
+                this.output = out;
+            else
+                this.output = new PrintStream(GFF_OUTPUT_FILE);
         }
         catch (Exception e)
         {
@@ -467,7 +480,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         try
         {
 	        this.output.flush();
-	        this.output.close();
+            if ( GFF_OUTPUT_FILE != null )
+                this.output.close();
         }
         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 1a9aa7c15..255c1c93a 100755
--- a/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
@@ -56,6 +56,8 @@ public class AlleleFrequencyEstimate {
                                             notes);
     }
 
+    public String toString() { return asTabularString(); }
+
     public String asString() {
         // Print out the called bases
         // Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref