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 74956feef..bc57f754f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -60,16 +60,17 @@ public class CycleCovariate implements StandardCovariate {
     // Used to pick out the covariate's value from attributes of the read
     public final Comparable getValue( final SAMRecord read, final int offset ) {
 
+        int cycle = 0;
+
         //-----------------------------
         // ILLUMINA
         //-----------------------------
 
         if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) ) {
-            int cycle = offset;
+            cycle = offset;
 	        if( read.getReadNegativeStrandFlag() ) {
 	            cycle = read.getReadLength() - (offset + 1);
 	        }
-	        return cycle;
         }
 
         //-----------------------------
@@ -77,7 +78,6 @@ public class CycleCovariate implements StandardCovariate {
         //-----------------------------
 
         else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
-            int cycle = 0;
             byte[] bases = read.getReadBases();
 
             // BUGBUG: Consider looking at degradation of base quality scores in homopolymer runs to detect when the cycle incremented even though the nucleotide didn't change
@@ -106,8 +106,6 @@ public class CycleCovariate implements StandardCovariate {
                     if( iii >= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii--; }
                 }
             }
-
-            return cycle;
         }
 
         //-----------------------------
@@ -120,7 +118,7 @@ public class CycleCovariate implements StandardCovariate {
 	        if( read.getReadNegativeStrandFlag() ) {
 	            pos = read.getReadLength() - (offset + 1);
 	        }
-        	return pos / 5; // integer division
+        	cycle = pos / 5; // integer division
         }
 
         //-----------------------------
@@ -142,6 +140,13 @@ public class CycleCovariate implements StandardCovariate {
             read.getReadGroup().setPlatform( defaultPlatform );
             return getValue( read, offset ); // a recursive call
         }
+
+        // TODO -- Ryan: sanity check me [EB]
+        // differentiate between first and second of pair
+        if ( read.getReadPairedFlag() && read.getSecondOfPairFlag() )
+            cycle *= -1;
+
+        return cycle;
     }
 
     // Used to get the covariate's value from input csv file in TableRecalibrationWalker
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 3436a075e..1fa61fbf1 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -16,10 +16,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariates1() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "16f87c9644b27c3c3fe7a963eed45d2d" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5a4873064e602e1f945f3881c6b4a3e5");
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "42f78368cc85eb3963329ad48c244e80" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f97ec61e98db1a580900d9f4985080d0" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "9eddef42ae847f2edd966d3a5b463e50" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "22ee532c7e521d8cbfabedb07673429d");
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "8b91c48f186c1e44723ac4e047ac553c" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f586fcd8642deae6504d39430b20b713" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -49,10 +49,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibrator1() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "d7f3e0db5ed9fefc917144a0f937d50d" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "1f1770363f381d06e8db9fead03ad7bb");
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "563cdb25b5a963121299ad319d5ec2ae" );
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "dd8b61060914b75199ca5babc60248fa" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "8d68e99f5ef1138f25893a6b2725d2e9" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5954b7246d2e0c5c65267026819d5933");
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "91fd3c557db56fd969523d8c06d71a0b" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "7dd4c6a3f318a1dccb3f33d08bff953b" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -80,7 +80,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "bc0e62dc366f2f6ca70847a832b4aad4");
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "79e6738031f5a6f993838b33d70716c3");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -108,7 +108,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "9d83a1653e076e028fecf4c2575f56e9" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "d6f3ea0cf2129ca5488977f087f1aa25" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -138,7 +138,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "8853add9cfd0a8171ca917b1c6452e0a" );
+        e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c0d5fdd6e07395ae2d7b08431995b30d" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();