/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* 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.
*/
package org.broadinstitute.gatk.engine.datasources.providers;
import org.testng.Assert;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.testng.annotations.Test;
import htsjdk.samtools.*;
import htsjdk.samtools.reference.ReferenceSequence;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* 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.
*/
/**
* User: hanna
* Date: May 27, 2009
* Time: 1:04:27 PM
*
*/
/**
* Test reading the reference for a given read.
*/
public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
/**
* tests that the ReadReferenceView correctly generates X's when a read overhangs the
* end of a contig
*/
@Test
public void testOverhangingRead() {
testOverhangingGivenSize(25,0);
testOverhangingGivenSize(25,12);
testOverhangingGivenSize(25,24);
}
/**
* a private method, that tests getting the read sequence for reads that overlap the end of the
* contig
* @param readLength the length of the read
* @param overlap the amount of overlap
*/
private void testOverhangingGivenSize(int readLength, int overlap) {
SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(sequenceFile.getSequenceDictionary().getSequences().size()-1);
final long contigStart = selectedContig.getSequenceLength() - (readLength - overlap - 1);
final long contigStop = selectedContig.getSequenceLength() + overlap;
ReadShardDataProvider dataProvider = new ReadShardDataProvider(null,genomeLocParser,null,sequenceFile,null);
ReadReferenceView view = new ReadReferenceView(dataProvider);
SAMRecord rec = buildSAMRecord(selectedContig.getSequenceName(),(int)contigStart,(int)contigStop);
ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(selectedContig.getSequenceName(),(int)contigStart,selectedContig.getSequenceLength());
//char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
byte[] expected = expectedAsSeq.getBases();
byte[] actual = view.getReferenceBases(rec);
Assert.assertEquals((readLength - overlap), expected.length);
Assert.assertEquals(readLength, actual.length);
int xRange = 0;
for (; xRange < (readLength - overlap); xRange++) {
Assert.assertTrue(actual[xRange] != 'X');
}
for (; xRange < actual.length; xRange++) {
Assert.assertTrue(actual[xRange] == 'X');
}
}
/**
* Compares the contents of the fasta and view at a specified location.
* @param loc the location to validate
*/
protected void validateLocation( GenomeLoc loc ) {
SAMRecord read = buildSAMRecord( loc.getContig(), (int)loc.getStart(), (int)loc.getStop() );
ReadShardDataProvider dataProvider = new ReadShardDataProvider(null,genomeLocParser,null,sequenceFile,null);
ReadReferenceView view = new ReadReferenceView(dataProvider);
ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(loc.getContig(),loc.getStart(),loc.getStop());
byte[] expected = expectedAsSeq.getBases();
byte[] actual = view.getReferenceBases(read);
org.testng.Assert.assertEquals(actual,expected,String.format("Base array at in shard %s does not match expected",loc.toString()));
}
/**
* Build a SAM record featuring the absolute minimum required dataset.
* TODO: Blatantly copied from LocusViewTemplate. Refactor these into a set of tools.
* @param contig Contig to populate.
* @param alignmentStart start of alignment
* @param alignmentEnd end of alignment
* @return New SAM Record
*/
protected SAMRecord buildSAMRecord( String contig, int alignmentStart, int alignmentEnd ) {
SAMFileHeader header = new SAMFileHeader();
header.setSequenceDictionary(sequenceFile.getSequenceDictionary());
SAMRecord record = new SAMRecord(header);
record.setReferenceIndex(sequenceFile.getSequenceDictionary().getSequenceIndex(contig));
record.setAlignmentStart(alignmentStart);
Cigar cigar = new Cigar();
cigar.add(new CigarElement(alignmentEnd-alignmentStart+1, CigarOperator.M));
record.setCigar(cigar);
return record;
}
}