diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index 987cac90e..f3124492c 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -533,7 +533,7 @@ public class SAMDataSource implements SimpleDataSource {
          */
         public SAMReaders(Reads sourceInfo) {
             for(File readsFile: sourceInfo.getReadsFiles()) {
-                SAMFileReader reader = new SAMFileReader(readsFile,true);
+                SAMFileReader reader = new SAMFileReader(readsFile);
                 reader.enableFileSource(true);
                 reader.enableIndexCaching(true);
                 reader.setValidationStringency(sourceInfo.getValidationStringency());
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 958004e84..fe2798aee 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod5() {
-        String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "18fca887d1eb7dc300e717ae03b9da62"};
+        String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "18fca887d1eb7dc300e717ae03b9da62"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod50() {
-        String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "9537e4f195ce5840136f60fb61201369"};
+        String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "9537e4f195ce5840136f60fb61201369"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerKnownsOnly() {
-        String[] md5s = {"d609430ffbc0fd8b68f383b9eec17e8b", "1091436c40d5ba557d85662999cc0c1d"};
+        String[] md5s = {"f50b9bddd78ed6fb820d2cbdfbff8300", "1091436c40d5ba557d85662999cc0c1d"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,