diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
index 86af70b21..a078aa42c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index 32c29a9d9..b14958f45 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -1,10 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
index d9f3c5557..098988cd9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 import java.util.HashMap;
 
 import org.broadinstitute.sting.utils.BaseUtils;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
index 035709262..11a9ec28c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
index 13bf5750c..c27cdafcd 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
index 451770af5..ef3349c80 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
@@ -1,8 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.Utils;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
index a1e033e03..dd71fc9c1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
@@ -1,9 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import org.broadinstitute.sting.utils.StingException;
-
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
index 894688885..bd9569c11 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
index 15cec3c1e..51095a30f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.SAMRecord;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *