Merge branch 'master' of github.com:broadinstitute/gsa-unstable
This commit is contained in:
Eric Banks
commit
4f243acaa6
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@ -34,6 +34,9 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
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private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
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private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
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// package access for unit testing
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ActivityProfile profile;
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@Override
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public String getTraversalUnits() {
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return "active regions";
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@ -53,7 +56,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
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int minStart = Integer.MAX_VALUE;
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final List<ActiveRegion> activeRegions = new LinkedList<ActiveRegion>();
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ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() );
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profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() );
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ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView);
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@ -277,8 +277,12 @@ public class VariantAnnotatorEngine {
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if ( expression.fieldName.equals("ID") ) {
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if ( vc.hasID() )
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infoAnnotations.put(expression.fullName, vc.getID());
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} else if (expression.fieldName.equals("ALT")) {
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infoAnnotations.put(expression.fullName, vc.getAlternateAllele(0).getDisplayString());
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} else if ( vc.hasAttribute(expression.fieldName) ) {
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infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
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infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
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}
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}
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}
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@ -190,6 +190,10 @@ public class UnifiedGenotyperEngine {
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final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
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if ( vc != null )
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results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap));
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// todo - uncomment if we want to also emit a null ref call (with no QUAL) if there's no evidence for REF and if EMIT_ALL_SITES is set
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// else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
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// results.add(generateEmptyContext(tracker, refContext, null, rawContext));
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}
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}
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}
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@ -183,6 +183,10 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
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@Argument(fullName="keepAC0", shortName="keepAC0", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
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private boolean keepSitesWithAC0 = false;
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@Hidden
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@Argument(fullName="numSamples", shortName="numSamples", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
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private int numSamplesFromArgument = 0;
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/**
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* If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
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* variant set, and evaluate the union of the results. Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
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@ -589,6 +593,14 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
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public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
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public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
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public int getNumberOfSamplesForEvaluation() {
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if (sampleNamesForEvaluation!= null && !sampleNamesForEvaluation.isEmpty())
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return sampleNamesForEvaluation.size();
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else {
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return numSamplesFromArgument;
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}
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}
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public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
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public List<RodBinding<VariantContext>> getComps() { return comps; }
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@ -29,7 +29,7 @@ public class AlleleCount extends VariantStratifier {
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// There are ploidy x n sample chromosomes
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// TODO -- generalize to handle multiple ploidy
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nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * getVariantEvalWalker().getSamplePloidy();
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nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy();
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if ( nchrom < 2 )
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throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");
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@ -103,6 +103,11 @@ public class ActivityProfile {
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isActiveList.add(result);
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}
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// for unit testing
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public List<ActivityProfileResult> getActiveList() {
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return isActiveList;
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}
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public int size() {
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return isActiveList.size();
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}
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@ -0,0 +1,126 @@
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package org.broadinstitute.sting.gatk.traversals;
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import org.testng.Assert;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceDictionary;
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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.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
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import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
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import org.broadinstitute.sting.gatk.datasources.reads.Shard;
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import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.executive.WindowMaker;
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import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
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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.activeregion.ActiveRegion;
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import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
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import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Created with IntelliJ IDEA.
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* User: thibault
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* Date: 11/13/12
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* Time: 2:47 PM
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*/
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public class TraverseActiveRegionsTest extends BaseTest {
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private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
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private final double prob;
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public DummyActiveRegionWalker() {
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this.prob = 1.0;
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}
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@Override
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public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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return new ActivityProfileResult(ref.getLocus(), prob);
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}
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@Override
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public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) {
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return 0;
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}
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@Override
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public Integer reduceInit() {
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return 0;
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}
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@Override
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public Integer reduce(Integer value, Integer sum) {
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return 0;
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}
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}
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private final TraverseActiveRegions<Integer, Integer> t = new TraverseActiveRegions<Integer, Integer>();
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private IndexedFastaSequenceFile reference;
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private GenomeLocParser genomeLocParser;
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private ActiveRegionWalker<Integer, Integer> walker;
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@BeforeClass
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private void init() throws FileNotFoundException {
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reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
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SAMSequenceDictionary dictionary = reference.getSequenceDictionary();
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genomeLocParser = new GenomeLocParser(dictionary);
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}
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@Test
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public void testAllIntervalsSeen() throws Exception {
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List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
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GenomeLoc interval = genomeLocParser.createGenomeLoc("1", 1, 1);
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intervals.add(interval);
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LocusShardDataProvider dataProvider = createDataProvider(intervals);
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t.traverse(walker, dataProvider, 0);
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boolean allGenomeLocsSeen = true;
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for (GenomeLoc loc : intervals) {
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boolean thisGenomeLocSeen = false;
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for (ActivityProfileResult active : t.profile.getActiveList()) {
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if (loc.equals(active.getLoc())) {
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thisGenomeLocSeen = true;
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break;
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}
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}
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if (!thisGenomeLocSeen) {
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allGenomeLocsSeen = false;
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break;
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}
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}
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Assert.assertTrue(allGenomeLocsSeen, "Some intervals missing from activity profile");
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}
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private LocusShardDataProvider createDataProvider(List<GenomeLoc> intervals) {
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walker = new DummyActiveRegionWalker();
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StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>());
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Shard shard = new MockLocusShard(genomeLocParser, intervals);
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WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser,iterator,shard.getGenomeLocs());
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WindowMaker.WindowMakerIterator window = windowMaker.next();
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GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
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//engine.setReferenceDataSource(reference);
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engine.setGenomeLocParser(genomeLocParser);
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t.initialize(engine);
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return new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
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}
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}
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