From 5f58492401b86a5dcf4cb3a615b90e12e07d8d94 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 Jan 2010 21:17:39 +0000
Subject: [PATCH] A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get
 through my previous bug fix. It should instead check the command line -maxQ
 argument.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/TableRecalibrationWalker.java | 5 ++---
 .../sting/utils/sam/ArtificialSAMFileWriter.java             | 2 +-
 .../recalibration/RecalibrationWalkersIntegrationTest.java   | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 7c57f9ded..bd709e2fe 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -94,7 +94,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
-    private static final String versionString = "v2.2.4"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.5"; // Major version, minor version, and build number
     private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
     private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
     private static final long RANDOM_SEED = 1032861495;
@@ -393,8 +393,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         }
 
         final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates;
-        return QualityUtils.boundQual( (int)Math.round(newQuality), QualityUtils.MAX_REASONABLE_Q_SCORE );
-
+        return QualityUtils.boundQual( (int)Math.round(newQuality), (byte)MAX_QUALITY_SCORE );
 
         // Verbose printouts used to validate with old recalibrator
         //if(key.contains(null)) {
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
index c60b430fd..9c2bb30e7 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
@@ -38,7 +38,7 @@ import java.util.List;
  *         <p/>
  *         Class ArtificialSAMFileWriter
  *         <p/>
- * generates a fike samwriter, that you can get the output reads
+ * generates a fake samwriter, that you can get the output reads
  * from when you're done.  
  */
 public class ArtificialSAMFileWriter implements SAMFileWriter {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index ecd74c118..ac61dddee 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -79,7 +79,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "c12b4fd5b4905cc632aa1da19be5c66a" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "bf8d62beda7d3cf38d660d7939901192" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();