When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java

@@ -4,17 +4,29 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
-/**
+/*
- * User: hanna
+ * Copyright (c) 2009 The Broad Institute
- * Date: May 22, 2009
- * Time: 12:24:23 PM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
  *
- * Users acknowledge that this software is supplied without any warranty or support.
+ * Permission is hereby granted, free of charge, to any person
- * The Broad Institute is not responsible for its use, misuse, or
+ * obtaining a copy of this software and associated documentation
- * functionality.
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 /**
@@ -65,10 +77,15 @@ public class LocusReferenceView extends ReferenceView {
      */
     public char[] getReferenceBases( GenomeLoc genomeLoc ) {
         long stop = genomeLoc.getStop();
-        if (reference.getSequence(genomeLoc.getContig()).length() > genomeLoc.getStart()) {
+        long other = reference.getSequence(genomeLoc.getContig()).length();
-            stop = reference.getSequence(genomeLoc.getContig()).length();
+        if (other < genomeLoc.getStop()) {
+            stop = other;
         }
         ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
+        if (genomeLoc.getStop() - stop < 0) {
+            int y = 0;
+            y++;
+        }
         return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
     }
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java

@@ -4,76 +4,100 @@ import org.junit.Test;
 import org.junit.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+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 net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
-/**
+/*
- * User: hanna
+ * Copyright (c) 2009 The Broad Institute
- * Date: May 27, 2009
- * Time: 11:10:00 AM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
  *
- * Users acknowledge that this software is supplied without any warranty or support.
+ * Permission is hereby granted, free of charge, to any person
- * The Broad Institute is not responsible for its use, misuse, or
+ * obtaining a copy of this software and associated documentation
- * functionality.
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-/**
+/** Tests for viewing the reference from the perspective of a locus. */
- * Tests for viewing the reference from the perspective of a locus.
- */
 
 public class LocusReferenceViewTest extends ReferenceViewTemplate {
-    /**
+    /** Multiple-base pair queries should generate exceptions. */
-     * Multiple-base pair queries should generate exceptions.
+    @Test(expected = InvalidPositionException.class)
-     */
-    @Test(expected=InvalidPositionException.class)
     public void testSingleBPFailure() {
-        Shard shard = new LocusShard( GenomeLocParser.createGenomeLoc(0,1,50) );
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, 1, 50));
 
-        ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
+        ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
         view.getReferenceBase(shard.getGenomeLoc());
     }
 
-    /**
+    @Test
-     * Queries outside the bounds of the shard should generate an error.
+    public void testOverlappingReferenceBases() {
-     */
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length()));
-    @Test(expected=InvalidPositionException.class)
-    public void testBoundsFailure() {
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0,1,50) );
 
-        ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
+        ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
-        view.getReferenceBase(GenomeLocParser.createGenomeLoc(0,51));
+        char[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
+        Assert.assertEquals(20, results.length);
+        for (int x = 0; x < results.length; x++) {
+            if (x <= 10) Assert.assertTrue(results[x] != 'X');
+            else Assert.assertTrue(results[x] == 'X');
+        }
+    }
+
+
+    /** Queries outside the bounds of the shard should generate an error. */
+    @Test(expected = InvalidPositionException.class)
+    public void testBoundsFailure() {
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, 1, 50));
+
+        ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
+        LocusReferenceView view = new LocusReferenceView(dataProvider);
+
+        view.getReferenceBase(GenomeLocParser.createGenomeLoc(0, 51));
     }
 
 
     /**
      * Compares the contents of the fasta and view at a specified location.
+     *
      * @param loc
      */
     protected void validateLocation( GenomeLoc loc ) {
-        Shard shard = new LocusShard( loc );
+        Shard shard = new LocusShard(loc);
         GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLoc());
 
-        ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
+        ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
-        while( shardIterator.hasNext() ) {
+        while (shardIterator.hasNext()) {
             GenomeLoc locus = shardIterator.next();
 
-            ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(),locus.getStart(),locus.getStop());
+            ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
             char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
             char actual = view.getReferenceBase(locus);
 
-            Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected",locus.toString(),shard.getGenomeLoc()),
+            Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLoc()),
                     expected,
                     actual);
         }