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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
This commit is contained in:
asivache 2010-03-22 17:37:52 +00:00
parent d2944461ef
commit ee1dc6092f
1 changed files with 9 additions and 4 deletions
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13
java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
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@ -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.Shard;
import org.broadinstitute.sting.gatk.datasources.shards.LocusShard; import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.StringUtil;
@ -57,7 +58,6 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
@Test @Test
public void testOverlappingReferenceBases() { public void testOverlappingReferenceBases() {
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length()))); 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); LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
LocusReferenceView view = new LocusReferenceView(dataProvider); 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. */ /** Queries outside the bounds of the shard should result in reference context window trimmed at the shard boundary. */
@Test(expected = InvalidPositionException.class) @Test
public void testBoundsFailure() { public void testBoundsFailure() {
Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, 1, 50))); Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, 1, 50)));
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null); LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, shard.getGenomeLocs().get(0), null, sequenceFile, null);
LocusReferenceView view = new LocusReferenceView(dataProvider); 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);
} }