From 2bd0b1bbf7279d0dd4e6ca03d8cff6dea13bf9c3 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Dec 2009 00:32:33 +0000
Subject: [PATCH] After further review, it's unclear that my patch in
 RecalDataManager was the right choice.  Reverting. Also updating other
 IntervalCleanerIntegrationTest failures that were masked by my first patch.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/recalibration/RecalDataManager.java  | 6 +++---
 .../gatk/walkers/indels/IntervalCleanerIntegrationTest.java | 6 +++---
 2 files changed, 6 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 cd2c74273..3bb6ee3f2 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -274,12 +274,12 @@ public class RecalDataManager {
                     if( read.getReadNegativeStrandFlag() ) {
                         readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
                     }
-                    byte[] inconsistency = new byte[readBases.length];
+                    int[] inconsistency = new int[readBases.length];
                     int iii;
                     byte prevBase = (byte) colorSpace[0]; // The sentinel
                     for( iii = 0; iii < readBases.length; iii++ ) {
                         byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
-                        inconsistency[iii] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
+                        inconsistency[iii] = ( thisBase == readBases[iii] ? 0 : 1 );
                         prevBase = readBases[iii];
                     }
                     read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
@@ -469,7 +469,7 @@ public class RecalDataManager {
      */
     public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
         if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) != null ) {
-            byte[] colorSpace = ((byte[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
+            int[] colorSpace = ((int[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
             return colorSpace[offset] != 0;
         } else {
             return false;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
index 8d008d763..0118d9b5b 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
@@ -16,18 +16,18 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
                  Arrays.asList(md5lod5));
         executeTest("testLod5", spec1);
 
-        String[] md5lod200 = {"1d89ee2af03df79eb5de494c77767221", "6137bf0c25c7972b07b0d3fc6979cf5b"};
+        String[] md5lod200 = {"32401cef2134d973ff0037df27f1dcca", "6137bf0c25c7972b07b0d3fc6979cf5b"};
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,
                  Arrays.asList(md5lod200));
         executeTest("testLod200", spec2);
 
-        String[] md5cleanedOnly = {"168c8d02fceb107477381b93d189fe1f", "460631e8d98644dcf53b3045ca40f02a"};
+        String[] md5cleanedOnly = {"7b5a6dcc0ee770f4c8e5d0d9f36a5c34", "460631e8d98644dcf53b3045ca40f02a"};
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,
                  Arrays.asList(md5cleanedOnly));
         executeTest("testCleanedOnly", spec3);
     }
-}
\ No newline at end of file
+}