From 45ebbf725c9f867f643fadb44b8326be3c06ce09 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 Apr 2011 21:12:05 +0000
Subject: [PATCH] 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
---
 .../sting/utils/GenomeLocParser.java           |  2 +-
 .../utils/interval/IntervalUtilsUnitTest.java  | 18 ++++++++++++++++++
 .../sting/queue/util/EmailMessage.scala        |  4 ++--
 .../MultiFullCallingPipelineTest.scala         |  4 ++--
 4 files changed, 23 insertions(+), 5 deletions(-)

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