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
This commit is contained in:
aaron
parent
47cb9f169e
commit
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@ -4,17 +4,29 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Utils;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.samtools.util.StringUtil;
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/**
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* User: hanna
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* Date: May 22, 2009
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* Time: 12:24:23 PM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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@ -65,10 +77,15 @@ public class LocusReferenceView extends ReferenceView {
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*/
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public char[] getReferenceBases( GenomeLoc genomeLoc ) {
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long stop = genomeLoc.getStop();
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if (reference.getSequence(genomeLoc.getContig()).length() > genomeLoc.getStart()) {
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stop = reference.getSequence(genomeLoc.getContig()).length();
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long other = reference.getSequence(genomeLoc.getContig()).length();
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if (other < genomeLoc.getStop()) {
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stop = other;
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}
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ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
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if (genomeLoc.getStop() - stop < 0) {
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int y = 0;
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y++;
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}
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return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
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}
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@ -4,76 +4,100 @@ import org.junit.Test;
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import org.junit.Assert;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.gatk.datasources.shards.Shard;
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import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
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import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.samtools.util.StringUtil;
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/**
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* User: hanna
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* Date: May 27, 2009
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* Time: 11:10:00 AM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* Tests for viewing the reference from the perspective of a locus.
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*/
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/** Tests for viewing the reference from the perspective of a locus. */
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public class LocusReferenceViewTest extends ReferenceViewTemplate {
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/**
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* Multiple-base pair queries should generate exceptions.
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*/
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@Test(expected=InvalidPositionException.class)
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/** Multiple-base pair queries should generate exceptions. */
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@Test(expected = InvalidPositionException.class)
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public void testSingleBPFailure() {
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Shard shard = new LocusShard( GenomeLocParser.createGenomeLoc(0,1,50) );
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Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, 1, 50));
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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view.getReferenceBase(shard.getGenomeLoc());
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}
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/**
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* Queries outside the bounds of the shard should generate an error.
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*/
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@Test(expected=InvalidPositionException.class)
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public void testBoundsFailure() {
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Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0,1,50) );
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@Test
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public void testOverlappingReferenceBases() {
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Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length()));
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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view.getReferenceBase(GenomeLocParser.createGenomeLoc(0,51));
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char[] results = view.getReferenceBases(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length() + 9));
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Assert.assertEquals(20, results.length);
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for (int x = 0; x < results.length; x++) {
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if (x <= 10) Assert.assertTrue(results[x] != 'X');
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else Assert.assertTrue(results[x] == 'X');
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}
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}
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/** Queries outside the bounds of the shard should generate an error. */
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@Test(expected = InvalidPositionException.class)
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public void testBoundsFailure() {
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Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, 1, 50));
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ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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view.getReferenceBase(GenomeLocParser.createGenomeLoc(0, 51));
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}
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/**
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* Compares the contents of the fasta and view at a specified location.
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*
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* @param loc
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*/
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protected void validateLocation( GenomeLoc loc ) {
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Shard shard = new LocusShard( loc );
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Shard shard = new LocusShard(loc);
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GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLoc());
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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while( shardIterator.hasNext() ) {
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while (shardIterator.hasNext()) {
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GenomeLoc locus = shardIterator.next();
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ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(),locus.getStart(),locus.getStop());
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ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
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char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
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char actual = view.getReferenceBase(locus);
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Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected",locus.toString(),shard.getGenomeLoc()),
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Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLoc()),
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expected,
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actual);
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}
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