Forgot to add file itself for new unit test
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Guillermo del Angel
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250adca350
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package org.broadinstitute.sting.gatk.walkers.genotyper;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMReadGroupRecord;
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import org.apache.commons.lang.ArrayUtils;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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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.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
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import java.util.*;
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import static org.testng.Assert.assertEquals;
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import static org.testng.Assert.assertTrue;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.BeforeSuite;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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/**
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* Created by IntelliJ IDEA.
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* User: delangel
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* Date: 3/22/12
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* Time: 11:24 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
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final int contigStart = 1;
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final int contigStop = 10;
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final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, contigStop-contigStart+1);
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final GATKSAMReadGroupRecord artificialGATKRG = new GATKSAMReadGroupRecord("synthetic");
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final String artificialContig = "chr1";
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final int artificialContigIndex = 0;
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final String artificialReadName = "synth";
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final int artificialRefStart = 1;
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final int artificialMappingQuality = 60;
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Map<String, SAMReadGroupRecord> sample2RG = new HashMap<String, SAMReadGroupRecord>();
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final String refBases = "AGGATACTGT";
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final String SAMPLE_PREFIX = "sample";
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List<String> sampleNames = new ArrayList<String>();
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final int nSamples = 1;
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final int numReadsPerAllele = 10;
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List<SAMReadGroupRecord> sampleRGs;
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private String sampleName(int i) { return sampleNames.get(i); }
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private SAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); }
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final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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final Logger logger = Logger.getLogger(Walker.class);
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final GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
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final IndelGenotypeLikelihoodsCalculationModel model = new IndelGenotypeLikelihoodsCalculationModel(UAC,logger);
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final int offset = 5;
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final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,offset,offset);
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final GenomeLoc window = genomeLocParser.createGenomeLoc(artificialContig,artificialRefStart,10);
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final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,this.refBases.getBytes());
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@BeforeSuite
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public void before() {
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sampleRGs = new ArrayList<SAMReadGroupRecord>();
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for ( int i = 0; i < nSamples; i++ ) {
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sampleNames.add(String.format("%s%04d", SAMPLE_PREFIX, i));
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SAMReadGroupRecord rg = createRG(sampleName(i));
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sampleRGs.add(rg);
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sample2RG.put(sampleName(i), rg);
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}
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}
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@Test
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public void testBasicConsensusCounts() {
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// 4 inserted bases, min cnt = 10
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String altBases = "CCTCCTGAGA";
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int eventLength = 4;
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List<Allele> alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases);
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Assert.assertEquals(alleles.size(),2);
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Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength));
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//altBases = "CCTCMTGAGA";
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eventLength = 3;
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alleles = getConsensusAlleles(eventLength,false,10,0.1, altBases);
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Assert.assertEquals(alleles.size(),2);
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Assert.assertEquals(alleles.get(0).getBaseString(), refBases.substring(offset,offset+eventLength));
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// same with min Reads = 11
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alleles = getConsensusAlleles(eventLength,false,11,0.1, altBases);
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Assert.assertEquals(alleles.size(),0);
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// increase required fraction per sample to just below threshold
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alleles = getConsensusAlleles(eventLength,false,10,0.49999, altBases);
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Assert.assertEquals(alleles.size(),2);
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alleles = getConsensusAlleles(eventLength,false,10,0.5001, altBases);
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Assert.assertEquals(alleles.size(),0);
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}
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private List<Allele> getConsensusAlleles(int eventLength, boolean isInsertion, int minCnt, double minFraction, String altBases) {
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final ConsensusAlleleCounter counter = new ConsensusAlleleCounter(genomeLocParser, true, minCnt, minFraction);
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return counter.computeConsensusAlleles(referenceContext,getContextFromAlleles(eventLength, isInsertion, altBases), AlignmentContextUtils.ReadOrientation.COMPLETE);
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}
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private Map<String,AlignmentContext> getContextFromAlleles(int eventLength, boolean isInsertion, String altBases) {
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// RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext);
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ArrayList vcAlleles = new ArrayList<Allele>();
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Allele refAllele, altAllele;
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if (isInsertion) {
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refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
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altAllele = Allele.create(altBases.substring(0,eventLength), false);
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}
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else {
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refAllele =Allele.create(refBases.substring(offset,offset+eventLength),true);
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altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
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}
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int stop = loc.getStart();
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vcAlleles.add(refAllele);
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vcAlleles.add(altAllele);
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final VariantContextBuilder builder = new VariantContextBuilder().source("");
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builder.loc(loc.getContig(), loc.getStart(), stop);
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builder.alleles(vcAlleles);
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builder.referenceBaseForIndel(referenceContext.getBase());
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builder.noGenotypes();
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final VariantContext vc = builder.make();
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Map<String,AlignmentContext> contexts = new HashMap<String,AlignmentContext>();
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for (String sample: sampleNames) {
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AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc,vc, altBases, numReadsPerAllele, sample));
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contexts.put(sample,context);
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}
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return contexts;
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}
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private SAMReadGroupRecord createRG(String name) {
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SAMReadGroupRecord rg = new SAMReadGroupRecord(name);
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rg.setPlatform("ILLUMINA");
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rg.setSample(name);
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return rg;
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}
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private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc, String altBases,
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int numReads, String sample) {
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List<PileupElement> pileupElements = new ArrayList<PileupElement>();
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int readStart = contigStart;
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int offset = (contigStop-contigStart+1)/2;
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int refAlleleLength = 0;
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int readCounter = 0;
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for (Allele allele: vc.getAlleles()) {
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if (allele.isReference())
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refAlleleLength = allele.getBases().length;
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int alleleLength = allele.getBases().length;
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for ( int d = 0; d < numReads; d++ ) {
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byte[] readBases = trueHaplotype(allele, offset, refAlleleLength);
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byte[] readQuals = new byte[readBases.length];
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Arrays.fill(readQuals,(byte)50);
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GATKSAMRecord read = new GATKSAMRecord(header);
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read.setBaseQualities(readQuals);
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read.setReadBases(readBases);
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read.setReadName(artificialReadName+readCounter++);
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boolean isBeforeDeletion = false, isBeforeInsertion = false;
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if (allele.isReference())
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read.setCigarString(readBases.length + "M");
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else {
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isBeforeDeletion = alleleLength<refAlleleLength;
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isBeforeInsertion = alleleLength>refAlleleLength;
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read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") +
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(readBases.length-offset)+"M");
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}
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int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0));
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read.setReadPairedFlag(false);
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read.setAlignmentStart(readStart);
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read.setMappingQuality(artificialMappingQuality);
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read.setReferenceName(loc.getContig());
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read.setReadNegativeStrandFlag(false);
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read.setAttribute("RG", sampleRG(sample).getReadGroupId());
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pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength));
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}
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}
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return new ReadBackedPileupImpl(loc,pileupElements);
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}
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byte[] trueHaplotype(Allele allele, int offset, int refAlleleLength) {
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// create haplotype based on a particular allele
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String prefix = refBases.substring(offset);
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String alleleBases = new String(allele.getBases());
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String postfix = refBases.substring(offset+refAlleleLength,refBases.length());
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return (prefix+alleleBases+postfix).getBytes();
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}
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}
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