Instead of always merging Picard interval files they are optionally merged by Sting Utils.

Disabled the MFCP while the FCP gets an update.
Minor updates to email messages for upcoming scala 2.9.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a

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

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);
+    }
 }

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]) = {
+  private def convert(addresses: List[String]): java.util.List[InternetAddress] = {
-    asJavaList(addresses.map(address => new InternetAddress(address, false)))
+    addresses.map(address => new InternetAddress(address, false))
   }
 
   override def toString = {

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")
+  @Test(dataProvider="datasets", enabled=false)
-  def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) = {
+  def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) {
     val projectName = dataset.name
     val testName = "MultiFullCallingPipeline-" + projectName