diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 670b90d43..439cd41f7 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -328,7 +328,7 @@ public class GenomeLocParser {
 
             // iterate through the list of merged intervals and add then as GenomeLocs
             List<GenomeLoc> ret = new ArrayList<GenomeLoc>();
-            for (Interval interval : il.getUniqueIntervals()) {
+            for (Interval interval : il.getIntervals()) {
                 ret.add(new GenomeLoc(interval.getSequence(), getContigIndex(interval.getSequence(),true), interval.getStart(), interval.getEnd()));
             }
             // always return null instead of empty list
diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
index 5a11bf17f..8bfbf2cdf 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
@@ -9,6 +9,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
@@ -393,4 +394,21 @@ public class IntervalUtilsUnitTest extends BaseTest {
         }
         return files;
     }
+
+    @DataProvider(name="unmergedIntervals")
+    public Object[][] getUnmergedIntervals() {
+        return new Object[][] {
+                new Object[] {"small_unmerged_picard_intervals.list"},
+                new Object[] {"small_unmerged_gatk_intervals.list"}
+        };
+    }
+
+    @Test(dataProvider="unmergedIntervals")
+    public void testUnmergedIntervals(String unmergedIntervals) {
+        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(genomeLocParser, Collections.singletonList(validationDataLocation + unmergedIntervals), false);
+        Assert.assertEquals(locs.size(), 2);
+
+        List<GenomeLoc> merged = genomeLocParser.mergeIntervalLocations(locs, IntervalMergingRule.ALL);
+        Assert.assertEquals(merged.size(), 1);
+    }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala b/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
index 4f865e0f1..cda981d29 100644
--- a/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
+++ b/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
@@ -114,8 +114,8 @@ class EmailMessage extends Logging {
    * @param addresses List of email addresses.
    * @return java.util.List of InternetAddress'es
    */
-  private def convert(addresses: List[String]) = {
-    asJavaList(addresses.map(address => new InternetAddress(address, false)))
+  private def convert(addresses: List[String]): java.util.List[InternetAddress] = {
+    addresses.map(address => new InternetAddress(address, false))
   }
 
   override def toString = {
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
index 2d81a6955..d19b59d41 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
@@ -54,8 +54,8 @@ class MultiFullCallingPipelineTest {
   final def convertDatasets: Array[Array[AnyRef]] =
     datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
 
-  @Test(dataProvider="datasets")
-  def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) = {
+  @Test(dataProvider="datasets", enabled=false)
+  def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) {
     val projectName = dataset.name
     val testName = "MultiFullCallingPipeline-" + projectName