From dcb7735d3c8cf8254f0bd80b42f827c654961ee0 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Wed, 2 Jan 2013 13:46:33 -0500
Subject: [PATCH 1/2] Active Region extensions must stay on contig

---
 .../traversals/TraverseActiveRegionsUnitTest.java | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java
index e82dc28e1..4cda1455e 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java
@@ -241,6 +241,21 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         Assert.assertEquals(intervalStops.size(), 0, "Interval stop location does not match an active region stop location");
     }
 
+    @Test
+    public void testActiveRegionExtensionOnContig() {
+        DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
+
+        Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values();
+        for (ActiveRegion activeRegion : activeRegions) {
+            GenomeLoc loc = activeRegion.getExtendedLoc();
+
+            // Contract: active region extensions must stay on the contig
+            Assert.assertTrue(loc.getStart() > 0, "Active region extension begins at location " + loc.getStart() + ", past the left end of the contig");
+            int refLen = dictionary.getSequence(loc.getContigIndex()).getSequenceLength();
+            Assert.assertTrue(loc.getStop() <= refLen, "Active region extension ends at location " + loc.getStop() + ", past the right end of the contig");
+        }
+    }
+
     @Test
     public void testPrimaryReadMapping() {
         DummyActiveRegionWalker walker = new DummyActiveRegionWalker();

From c515175313e802bdc7b9e87df6d1498897c2ee1a Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Wed, 2 Jan 2013 14:10:55 -0500
Subject: [PATCH 2/2] Ensure that active region extensions stay on contig

---
 .../src/org/broadinstitute/sting/utils/GenomeLocParser.java  | 5 +++++
 .../sting/utils/activeregion/ActiveRegion.java               | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index dbffacfbc..c18eef23f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -287,6 +287,11 @@ public final class GenomeLocParser {
         return new GenomeLoc(contig, index, start, stop);
     }
 
+    public GenomeLoc createGenomeLocOnContig(final String contig, final int start, final int stop) {
+        GenomeLoc contigLoc = createOverEntireContig(contig);
+        return new GenomeLoc(contig, getContigIndex(contig), start, stop).intersect(contigLoc);
+    }
+
     /**
      * validate a position or interval on the genome as valid
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index 0d12d53cc..c12dfcee9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -31,7 +31,7 @@ public class ActiveRegion implements HasGenomeLocation {
         this.isActive = isActive;
         this.genomeLocParser = genomeLocParser;
         this.extension = extension;
-        extendedLoc = genomeLocParser.createGenomeLoc(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
+        extendedLoc = genomeLocParser.createGenomeLocOnContig(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
         fullExtentReferenceLoc = extendedLoc;
     }