From df998041a829e2f783fc150038a589b071910256 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 Jan 2010 16:31:25 +0000
Subject: [PATCH] Minor change to solid warning message. Added note for a
 future solid recalibration integration test when we get the required data
 file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/RecalDataManager.java    | 14 ++++++++------
 .../RecalibrationWalkersIntegrationTest.java       |  3 +++
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 41ed957b7..9c88e46db 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -57,7 +57,7 @@ public class RecalDataManager {
     private static boolean warnUserNullReadGroup = false;
     private static boolean warnUserNoColorSpace = false;
 
-    public static final String versionString = "v2.2.10"; // Major version, minor version, and build number
+    public static final String versionString = "v2.2.11"; // Major version, minor version, and build number
 
     RecalDataManager() {
     	data = new NestedHashMap();
@@ -251,6 +251,7 @@ public class RecalDataManager {
      * @param read The SAMRecord to parse
      */
     public static void parseColorSpace( final SAMRecord read ) {
+
         // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
         if( read.getReadGroup().getPlatform().equalsIgnoreCase("SOLID") ) {
             if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null ) { // Haven't calculated the inconsistency array yet for this read
@@ -279,8 +280,8 @@ public class RecalDataManager {
                     read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
 
                 } else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag
-                    Utils.warnUser("Unable to find color space information in SOLID read. First observed at read with name = " + read.getReadName());
-                    Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into the SOLID read. Are you sure you want to proceed?");
+                    Utils.warnUser("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName());
+                    Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into SOLiD reads. Are you sure you want to proceed?");
                     warnUserNoColorSpace = true;
                 }
             }
@@ -337,14 +338,14 @@ public class RecalDataManager {
             } 
 
         } else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag
-            Utils.warnUser("Unable to find color space information in SOLID read. First observed at read with name = " + read.getReadName());
-            Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into the SOLID read. Are you sure you want to proceed?");
+            Utils.warnUser("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName());
+            Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into SOLiD reads. Are you sure you want to proceed?");
             warnUserNoColorSpace = true;
         }
+
         return originalQualScores;
     }
 
-
     /**
      * Perform the SET_Q_ZERO solid recalibration. Inconsistent color space bases and their previous base are set to quality zero
      * @param read The SAMRecord to recalibrate
@@ -378,6 +379,7 @@ public class RecalDataManager {
             readBases = BaseUtils.simpleReverseComplement( readBases.clone() ); // Put the bases back in reverse order to stuff them back in the read
         }
         read.setReadBases( readBases );
+
         return originalQualScores;
     }
 
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 901819f5f..971e5a8f1 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -107,6 +107,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
+    //TODO -- Add an integration test which tests SOLiD files that contain indels to make sure the Cigar string is processed correctly in the solid_recal_modes
+    // Currently we don't have any such data
+
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();