diff --git a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
index f3f5db8a0..ed6e09a8d 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
@@ -82,6 +82,14 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
         sanityCheckDictionaryAgainstIndex();
     }
 
+    /**
+     * Always returns true for this implementation.
+     * @return True.
+     */
+    public boolean isIndexed() {
+        return true;
+    }
+
     /**
      * Loads a dictionary, if available.
      * @param fastaFile File to check for a match.
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
index e6abcdbbb..0dd1dec81 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
@@ -278,10 +278,20 @@ public abstract class LocusViewTemplate extends BaseTest {
                 return dictionary;
             }
 
+            public boolean isIndexed() { return false; }
+
             public ReferenceSequence nextSequence() {
                 throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
             }
 
+            public ReferenceSequence getSequence( String contig ) {
+                throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
+            }
+
+            public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
+                throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
+            }
+
             public void reset() {
                 return;
             }
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar b/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar
deleted file mode 100644
index 439153e5f..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1432.jar b/settings/repository/edu.mit.broad/picard-private-parts-1432.jar
new file mode 100644
index 000000000..c89efd5eb
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-1432.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml b/settings/repository/edu.mit.broad/picard-private-parts-1432.xml
similarity index 55%
rename from settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1432.xml
index 3c2c86322..b7d87ec0a 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1432.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1409-sharding" status="integration" publication="20100606141600" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1432" status="integration" publication="20100616174700" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.19.430-sharding.xml b/settings/repository/net.sf/picard-1.19.430-sharding.xml
deleted file mode 100644
index d3a705294..000000000
--- a/settings/repository/net.sf/picard-1.19.430-sharding.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.19.430-sharding" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.19.430-sharding.jar b/settings/repository/net.sf/picard-1.22.448.jar
similarity index 69%
rename from settings/repository/net.sf/picard-1.19.430-sharding.jar
rename to settings/repository/net.sf/picard-1.22.448.jar
index 836e02e70..b4e68d37a 100644
Binary files a/settings/repository/net.sf/picard-1.19.430-sharding.jar and b/settings/repository/net.sf/picard-1.22.448.jar differ
diff --git a/settings/repository/net.sf/picard-1.22.448.xml b/settings/repository/net.sf/picard-1.22.448.xml
new file mode 100644
index 000000000..e9b5359d2
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.22.448.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.22.448" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.19.430-sharding.xml b/settings/repository/net.sf/sam-1.19.430-sharding.xml
deleted file mode 100644
index a6fb4a33b..000000000
--- a/settings/repository/net.sf/sam-1.19.430-sharding.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.19.430-sharding" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.19.430-sharding.jar b/settings/repository/net.sf/sam-1.22.448.jar
similarity index 76%
rename from settings/repository/net.sf/sam-1.19.430-sharding.jar
rename to settings/repository/net.sf/sam-1.22.448.jar
index f80aadb6f..82fa9729c 100644
Binary files a/settings/repository/net.sf/sam-1.19.430-sharding.jar and b/settings/repository/net.sf/sam-1.22.448.jar differ
diff --git a/settings/repository/net.sf/sam-1.22.448.xml b/settings/repository/net.sf/sam-1.22.448.xml
new file mode 100644
index 000000000..186f70023
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.22.448.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.22.448" status="release" />
+</ivy-module>