From ca9cd9b688cfd23804e341daea0fe409f4278d7f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 6 Oct 2011 22:38:44 -0400
Subject: [PATCH] Minor fix for merging intervals which hadn't been necessary
 when only merging from the left to right.  Added integration tests to cover
 the parallelization of RTC.

---
 .../indels/RealignerTargetCreator.java        |  4 +++
 ...RealignerTargetCreatorIntegrationTest.java | 33 +++++++++++++++----
 2 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index e1333b7f2..56ce60449 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -415,6 +415,10 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
                             eventStartPos = lastPosition;
                         else
                             eventStartPos = Math.min(eventStartPos, lastPosition);
+                    } else if ( eventStartPos == -1 && e.eventStartPos != -1 ) {
+                        eventStartPos = e.eventStartPos;
+                        eventStopPos = e.eventStopPos;
+                        furthestStopPos = e.furthestStopPos;
                     }
                 }
                 pointEvents.add(newPosition);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index fdb310428..78b24d646 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -8,20 +8,41 @@ import java.util.Arrays;
 public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
 
     @Test
-    public void testIntervals() {
+    public void testIntervals1() {
+        String md5 = "3f0b63a393104d0c4158c7d1538153b8";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
                  1,
-                 Arrays.asList("3f0b63a393104d0c4158c7d1538153b8"));
-        executeTest("test standard", spec1);
+                 Arrays.asList(md5));
+        executeTest("test standard nt=1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
+                "-nt 4 -T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
                  1,
-                 Arrays.asList("5085054c78e256432dc75c85a9ac631c"));
-        executeTest("test dbsnp", spec2);
+                 Arrays.asList(md5));
+        executeTest("test standard nt=4", spec2);
+    }
 
+    @Test
+    public void testIntervals2() {
+        String md5 = "e0f745b79b679c225314a2abef4919ff";
+
+        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
+                "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
+                 1,
+                 Arrays.asList(md5));
+        executeTest("test with dbsnp nt=1", spec1);
+
+        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
+                "-nt 4 -T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
+                 1,
+                 Arrays.asList(md5));
+        executeTest("test with dbsnp nt=4", spec2);
+    }
+
+    @Test
+    public void testKnownsOnly() {
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
                 "-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI known -o %s",
                  1,