diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index a7ec40101..7cf53fc11 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -580,4 +580,8 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
     protected long position() {
         return mFileBuffer.position();
     }
+
+    @Override
+    public void close() {
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index 31b8ae996..3829636fc 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -752,6 +752,7 @@ public class SAMDataSource {
             for(SAMReaderID readerID: readerIDs) {
                 SAMFileReader reader = new SAMFileReader(readerID.samFile);
                 reader.enableFileSource(true);
+                reader.enableIndexMemoryMapping(false);
                 if(!enableLowMemorySharding)
                     reader.enableIndexCaching(true);
                 reader.setValidationStringency(validationStringency);
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1702.jar b/settings/repository/edu.mit.broad/picard-private-parts-1816.jar
similarity index 56%
rename from settings/repository/edu.mit.broad/picard-private-parts-1702.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1816.jar
index 1f8a5c047..33238a46f 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1702.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1816.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1702.xml b/settings/repository/edu.mit.broad/picard-private-parts-1816.xml
similarity index 64%
rename from settings/repository/edu.mit.broad/picard-private-parts-1702.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1816.xml
index 87daf0c38..a2dad75a1 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1702.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1816.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1702" status="integration" publication="20110102175300" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1816" status="integration" publication="20110102175300" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.37.686.xml b/settings/repository/net.sf/picard-1.37.686.xml
deleted file mode 100644
index 174345540..000000000
--- a/settings/repository/net.sf/picard-1.37.686.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.37.686" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.37.686.jar b/settings/repository/net.sf/picard-1.42.773.jar
similarity index 72%
rename from settings/repository/net.sf/picard-1.37.686.jar
rename to settings/repository/net.sf/picard-1.42.773.jar
index 7ae927cb2..4280f2cfb 100644
Binary files a/settings/repository/net.sf/picard-1.37.686.jar and b/settings/repository/net.sf/picard-1.42.773.jar differ
diff --git a/settings/repository/net.sf/picard-1.42.773.xml b/settings/repository/net.sf/picard-1.42.773.xml
new file mode 100644
index 000000000..3ccf0dd2f
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.42.773.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.42.773" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.37.686.xml b/settings/repository/net.sf/sam-1.37.686.xml
deleted file mode 100644
index df9147198..000000000
--- a/settings/repository/net.sf/sam-1.37.686.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.37.686" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.37.686.jar b/settings/repository/net.sf/sam-1.42.773.jar
similarity index 76%
rename from settings/repository/net.sf/sam-1.37.686.jar
rename to settings/repository/net.sf/sam-1.42.773.jar
index 44a4ac383..75f280d17 100644
Binary files a/settings/repository/net.sf/sam-1.37.686.jar and b/settings/repository/net.sf/sam-1.42.773.jar differ
diff --git a/settings/repository/net.sf/sam-1.42.773.xml b/settings/repository/net.sf/sam-1.42.773.xml
new file mode 100644
index 000000000..53d6d3eab
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.42.773.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.42.773" status="release" />
+</ivy-module>