diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index aef85d491..227a652a0 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -384,7 +384,7 @@ public class GenomeAnalysisEngine {
             rg_sets.add(groups);
 
             for (SAMReadGroupRecord g : r.getFileHeader().getReadGroups()) {
-                if (hm.hasGroupIdDuplicates()) { // Check if there were read group clashes with hasGroupIdDuplicates and if so:
+                if (hm.hasReadGroupCollisions()) { // Check if there were read group clashes with hasGroupIdCollisions and if so:
                     // use HeaderMerger to translate original read group id from the reader into the read group id in the
                     // merged stream, and save that remapped read group id to associate it with specific reader
                     groups.add(hm.getReadGroupId(r, g.getReadGroupId()));
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 265df5879..f826cc59c 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -235,7 +235,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         final SAMRecord record = iterator.next();
         addIfNotEmpty(iterator);
 
-        if (this.samHeaderMerger.hasGroupIdDuplicates()) {
+        if (this.samHeaderMerger.hasReadGroupCollisions()) {
             final String id = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
             final String newId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), id);
             record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newId);
diff --git a/settings/repository/edu.mit.broad/picard-private-1084.jar b/settings/repository/edu.mit.broad/picard-private-1105.jar
similarity index 81%
rename from settings/repository/edu.mit.broad/picard-private-1084.jar
rename to settings/repository/edu.mit.broad/picard-private-1105.jar
index 66dce1a99..e4f49d57e 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-1084.jar and b/settings/repository/edu.mit.broad/picard-private-1105.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-1084.xml b/settings/repository/edu.mit.broad/picard-private-1105.xml
similarity index 63%
rename from settings/repository/edu.mit.broad/picard-private-1084.xml
rename to settings/repository/edu.mit.broad/picard-private-1105.xml
index 18204e9a7..aeaf508ca 100644
--- a/settings/repository/edu.mit.broad/picard-private-1084.xml
+++ b/settings/repository/edu.mit.broad/picard-private-1105.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="1105" status="integration" publication="20091110205100" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.05.140.xml b/settings/repository/net.sf/picard-1.05.140.xml
deleted file mode 100644
index aac545236..000000000
--- a/settings/repository/net.sf/picard-1.05.140.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<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/picard-1.05.140.jar b/settings/repository/net.sf/picard-1.07.165.jar
similarity index 66%
rename from settings/repository/net.sf/picard-1.05.140.jar
rename to settings/repository/net.sf/picard-1.07.165.jar
index b93c47700..aa93c00b1 100644
Binary files a/settings/repository/net.sf/picard-1.05.140.jar and b/settings/repository/net.sf/picard-1.07.165.jar differ
diff --git a/settings/repository/net.sf/picard-1.07.165.xml b/settings/repository/net.sf/picard-1.07.165.xml
new file mode 100644
index 000000000..33f651303
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.07.165.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.07.165" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.05.140.xml b/settings/repository/net.sf/sam-1.05.140.xml
deleted file mode 100644
index a9e5a57b2..000000000
--- a/settings/repository/net.sf/sam-1.05.140.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.05.140" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.05.140.jar b/settings/repository/net.sf/sam-1.07.165.jar
similarity index 82%
rename from settings/repository/net.sf/sam-1.05.140.jar
rename to settings/repository/net.sf/sam-1.07.165.jar
index e983077fd..cc710b855 100644
Binary files a/settings/repository/net.sf/sam-1.05.140.jar and b/settings/repository/net.sf/sam-1.07.165.jar differ
diff --git a/settings/repository/net.sf/sam-1.07.165.xml b/settings/repository/net.sf/sam-1.07.165.xml
new file mode 100644
index 000000000..1fd90c4f9
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.07.165.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.07.165" status="release" />
+</ivy-module>