diff --git a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
index 4dc2f1bc5..2262f12b2 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
@@ -70,7 +70,8 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
 
         try {
             final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
-            final SAMFileHeader header = codec.decode(new AsciiLineReader(new FileInputStream(dictionary)), dictionary);
+            final SAMFileHeader header = codec.decode(new AsciiLineReader(new FileInputStream(dictionary)),
+                                                      dictionary.toString());
             if (header.getSequenceDictionary() != null && header.getSequenceDictionary().size() > 0) {
                 this.sequenceDictionary = header.getSequenceDictionary();
             }
diff --git a/settings/repository/edu.mit.broad/picard-private-1060.jar b/settings/repository/edu.mit.broad/picard-private-1084.jar
similarity index 73%
rename from settings/repository/edu.mit.broad/picard-private-1060.jar
rename to settings/repository/edu.mit.broad/picard-private-1084.jar
index 3aa9000ba..66dce1a99 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-1060.jar and b/settings/repository/edu.mit.broad/picard-private-1084.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-1060.xml b/settings/repository/edu.mit.broad/picard-private-1084.xml
similarity index 63%
rename from settings/repository/edu.mit.broad/picard-private-1060.xml
rename to settings/repository/edu.mit.broad/picard-private-1084.xml
index a2b7786c3..18204e9a7 100644
--- a/settings/repository/edu.mit.broad/picard-private-1060.xml
+++ b/settings/repository/edu.mit.broad/picard-private-1084.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="1060" status="integration" publication="20090930104500" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.04.xml b/settings/repository/net.sf/picard-1.04.xml
deleted file mode 100644
index 8b24bb9b9..000000000
--- a/settings/repository/net.sf/picard-1.04.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.04" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.04.jar b/settings/repository/net.sf/picard-1.05.140.jar
similarity index 82%
rename from settings/repository/net.sf/picard-1.04.jar
rename to settings/repository/net.sf/picard-1.05.140.jar
index 91b8fb1bb..b93c47700 100644
Binary files a/settings/repository/net.sf/picard-1.04.jar and b/settings/repository/net.sf/picard-1.05.140.jar differ
diff --git a/settings/repository/net.sf/picard-1.05.140.xml b/settings/repository/net.sf/picard-1.05.140.xml
new file mode 100644
index 000000000..aac545236
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.05.140.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.05.140" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.04.xml b/settings/repository/net.sf/sam-1.04.xml
deleted file mode 100644
index 4e36a4f49..000000000
--- a/settings/repository/net.sf/sam-1.04.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.04" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.04.jar b/settings/repository/net.sf/sam-1.05.140.jar
similarity index 79%
rename from settings/repository/net.sf/sam-1.04.jar
rename to settings/repository/net.sf/sam-1.05.140.jar
index 3cff3bd3a..e983077fd 100644
Binary files a/settings/repository/net.sf/sam-1.04.jar and b/settings/repository/net.sf/sam-1.05.140.jar differ
diff --git a/settings/repository/net.sf/sam-1.05.140.xml b/settings/repository/net.sf/sam-1.05.140.xml
new file mode 100644
index 000000000..a9e5a57b2
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.05.140.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.05.140" status="release" />
+</ivy-module>