From ee1dc6092f5540f0337b9e6f0758ee9a3e92521c Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 22 Mar 2010 17:37:52 +0000
Subject: [PATCH] Test updated. Now we do not throw an exception when locus
 interval is out of bounds, we just return silently a reference context
 trimmed to the current shard boundaries. New test checks for trimming.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../providers/LocusReferenceViewTest.java           | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
index 9aef9e56a..e5cc7956b 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
@@ -8,6 +8,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
 import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
@@ -57,7 +58,6 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
     @Test
     public void testOverlappingReferenceBases() {
         Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length())));
-
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
@@ -70,15 +70,20 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
     }
 
 
-    /** Queries outside the bounds of the shard should generate an error. */
-    @Test(expected = InvalidPositionException.class)
+    /** Queries outside the bounds of the shard should result in reference context window trimmed at the shard boundary. */
+    @Test
     public void testBoundsFailure() {
         Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, 1, 50)));
 
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
-        view.getReferenceContext(GenomeLocParser.createGenomeLoc(0, 51)).getBase();
+        GenomeLoc locus = GenomeLocParser.createGenomeLoc(0, 50, 51);
+
+        ReferenceContext rc = view.getReferenceContext(locus);
+        Assert.assertTrue(rc.getLocus().equals(locus));
+        Assert.assertTrue(rc.getWindow().equals(GenomeLocParser.createGenomeLoc(0,50)));
+        Assert.assertTrue(rc.getBases().length == 1);
     }