From 24722a442e43767fd84a9ef3bc133c5f96382329 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Apr 2009 22:21:36 +0000
Subject: [PATCH] Slight code cleanup

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/walkers/PileupWalker.java  | 2 +-
 .../sting/gatk/walkers/ValidatingPileupWalker.java           | 2 +-
 .../sting/playground/gatk/walkers/AlleleFrequencyWalker.java | 5 ++++-
 .../src/org/broadinstitute/sting/utils/ReadBackedPileup.java | 4 ++--
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index befed2ab7..383bfd936 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -36,7 +36,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
     }
 
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
-        ReadBackedPileup pileup = new ReadBackedPileup(context.getLocation(), ref, context);
+        ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
         String bases = pileup.getBases();
         
         if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
index 684fa937e..2fd8542cd 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
@@ -20,7 +20,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
     public boolean VERBOSE;
 
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
-        ReadBackedPileup pileup = new ReadBackedPileup(context.getLocation(), ref, context);
+        ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
 
         rodSAMPileup truePileup = (rodSAMPileup)tracker.lookup("pileup", null);
         if ( truePileup == null )
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 cd926b711..1c339860c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -62,7 +62,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         this.initalize();
 
         // Convert context data into bases and 4-base quals
-        String bases     = getBases(context);
+        Pileup pileup    = new ReadBackedPileup(ref, context);
+        String bases     = pileup.getBases();
         double quals[][] = getQuals(context);
         //String[] indels  = getIndels(context);
 
@@ -143,6 +144,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         return alleleFreq;
     }
 
+    /*
     static public String getBases (LocusContext context)
     {
         // Convert bases to CharArray
@@ -159,6 +161,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
         }
         return new String(bases);
     }
+    */
 
     /*
     static public String[] getIndels(LocusContext context)
diff --git a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
index feeb97faf..a34831b29 100755
--- a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
@@ -19,8 +19,8 @@ public class ReadBackedPileup extends BasicPileup {
     List<SAMRecord> reads;
     List<Integer> offsets;
 
-    public ReadBackedPileup(GenomeLoc loc, char ref, LocusContext context ) {
-        this(loc, ref, context.getReads(), context.getOffsets());
+    public ReadBackedPileup(char ref, LocusContext context ) {
+        this(context.getLocation(), ref, context.getReads(), context.getOffsets());
     }
 
     public ReadBackedPileup(GenomeLoc loc, char ref, List<SAMRecord> reads, List<Integer> offsets ) {