From 7e7c83ddcac567f28a543ec530ef0b0eb10be490 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 2 Jun 2009 18:33:45 +0000
Subject: [PATCH] fixing insidious bugs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/LogisticRecalibrationWalker.java  | 4 ++--
 java/src/org/broadinstitute/sting/utils/BaseUtils.java        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
index 0c7344366..0fef7b817 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
@@ -17,7 +17,7 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
     public String logisticParamsFile;
 
     @Argument(shortName="outputBAM", doc="output BAM file", required=false)
-    public String outputBamFile = "";
+    public String outputBamFile = null;
 
     HashMap<String, LogisticRegressor> regressors = new HashMap<String, LogisticRegressor>();
     private static Logger logger = Logger.getLogger(LogisticRecalibrationWalker.class);
@@ -120,7 +120,7 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
                 //newQual = QualityUtils.probToQual(P);
 
                 //newQual = (byte)Math.min(Math.round(-10*logPOver1minusP),63);
-                //System.out.printf("Recal %s %d %d => %f => %f leads to %d%n", dinuc, cycle, qual, logPOver1minusP, P, newQual);
+                //System.out.printf("Recal %s %d %d %d%n", dinuc, cycle, qual, newQual);
             }else{
                 newQual = qual;
             }
diff --git a/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index bb6b4b1c9..2691c0164 100644
--- a/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -184,7 +184,7 @@ public class BaseUtils {
         byte[] rcbases = new byte[bases.length];
 
         for (int i = 0; i < bases.length; i++) {
-            rcbases[i] = bases[bases.length - 1];
+            rcbases[i] = bases[bases.length - i - 1];
         }
 
         return rcbases;