From 7732f98e56b432177abd75fe35e36da645269a56 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 Jan 2010 20:09:16 +0000
Subject: [PATCH] Fix for Solid reads that have '.' in their color space field.
 The recalibrator will just set them to be illumina reads and won't apply
 color space correction.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2661 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/RecalDataManager.java   | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

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 114b2672b..1ccf40a13 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -259,12 +259,16 @@ public class RecalDataManager {
                 if( attr != null ) {
                     char[] colorSpace;
                     if( attr instanceof String ) {
+                        if( ((String)attr).contains(".") ) { // empty color space, abort
+                            read.getReadGroup().setPlatform("illumina");
+                            return;
+                        }
                         colorSpace = ((String)attr).toCharArray();
                     } else {
                         throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
                     }
 
-                    // Loop over the read and calculate first the infered bases from the color and then check if it is consistent with the read
+                    // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
                     byte[] readBases = read.getReadBases();
                     if( read.getReadNegativeStrandFlag() ) {
                         readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
@@ -304,6 +308,10 @@ public class RecalDataManager {
         if( attr != null ) {
             char[] colorSpace;
             if( attr instanceof String ) {
+                if( ((String)attr).contains(".") ) { // empty color space, abort
+                    read.getReadGroup().setPlatform("illumina");
+                    return originalQualScores;
+                }
                 colorSpace = ((String)attr).toCharArray();
             } else {
                 throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));