diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index ca865eef1..c440930cf 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -184,7 +184,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
 
         record.setHeader(samHeaderMerger.getMergedHeader());
         if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() >= 0) {
-            record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
+            record.setReferenceIndex(this.samHeaderMerger.getMergedSequenceIndex(iterator.getReader(),record.getReferenceIndex()));
         }
         
         //System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());
diff --git a/settings/repository/edu.mit.broad/picard-private-771.jar b/settings/repository/edu.mit.broad/picard-private-801.jar
similarity index 64%
rename from settings/repository/edu.mit.broad/picard-private-771.jar
rename to settings/repository/edu.mit.broad/picard-private-801.jar
index 07f7262bd..6d017a8fc 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-771.jar and b/settings/repository/edu.mit.broad/picard-private-801.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-771.xml b/settings/repository/edu.mit.broad/picard-private-801.xml
similarity index 62%
rename from settings/repository/edu.mit.broad/picard-private-771.xml
rename to settings/repository/edu.mit.broad/picard-private-801.xml
index 9120743dc..c60d56a3f 100644
--- a/settings/repository/edu.mit.broad/picard-private-771.xml
+++ b/settings/repository/edu.mit.broad/picard-private-801.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="771" status="integration" publication="20090528143800" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="801" status="integration" publication="20090102400000" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.01.26.xml b/settings/repository/net.sf/picard-1.01.26.xml
deleted file mode 100644
index 4edbe7050..000000000
--- a/settings/repository/net.sf/picard-1.01.26.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.01.26" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.01.26.jar b/settings/repository/net.sf/picard-1.01.38.jar
similarity index 75%
rename from settings/repository/net.sf/picard-1.01.26.jar
rename to settings/repository/net.sf/picard-1.01.38.jar
index c03d34295..356a2084c 100644
Binary files a/settings/repository/net.sf/picard-1.01.26.jar and b/settings/repository/net.sf/picard-1.01.38.jar differ
diff --git a/settings/repository/net.sf/picard-1.01.38.xml b/settings/repository/net.sf/picard-1.01.38.xml
new file mode 100644
index 000000000..adfc8590d
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.01.38.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.01.38" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.0.26.xml b/settings/repository/net.sf/sam-1.0.26.xml
deleted file mode 100644
index c0d9b102b..000000000
--- a/settings/repository/net.sf/sam-1.0.26.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.0.26" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.0.26.jar b/settings/repository/net.sf/sam-1.0.38.jar
similarity index 67%
rename from settings/repository/net.sf/sam-1.0.26.jar
rename to settings/repository/net.sf/sam-1.0.38.jar
index 93f1ebbdd..809ca0f59 100644
Binary files a/settings/repository/net.sf/sam-1.0.26.jar and b/settings/repository/net.sf/sam-1.0.38.jar differ
diff --git a/settings/repository/net.sf/sam-1.0.38.xml b/settings/repository/net.sf/sam-1.0.38.xml
new file mode 100644
index 000000000..2de347bf7
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.0.38.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.0.38" status="release" />
+</ivy-module>