diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index b0c4e203b..da7eaf6e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -689,8 +689,6 @@ public class GenomeAnalysisEngine {
         validateSuppliedReads();
         readsDataSource = createReadsDataSource(argCollection,genomeLocParser,referenceDataSource.getReference());
 
-        sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
-
         for (ReadFilter filter : filters)
             filter.initialize(this);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
index 3046ef925..98331ec1d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
@@ -223,8 +223,10 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
     @Override
     public void initialize() {
-        if ( getToolkit().getSamples().size() > 1 )
+        if ( getToolkit().getSamples().size() != 2 ) {
+            // unbelievably there are actually two samples even when there's just one in the header.  God I hate this Samples system
             throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
+        }
 
         try {
             PrintStream summaryOut = new PrintStream(summaryFile);