Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
aab0ec209b
commit
fd8dd8fb9b
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@ -100,7 +100,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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private Set<String> compNames = new TreeSet<String>();
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private Set<String> knownNames = new TreeSet<String>();
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private Set<String> evalNames = new TreeSet<String>();
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private Set<String> sampleNames = new TreeSet<String>();
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private Set<String> sampleNamesForEvaluation = new TreeSet<String>();
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private Set<String> sampleNamesForStratification = new TreeSet<String>();
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private int numSamples = 0;
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// The list of stratifiers and evaluators to use
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@ -186,7 +188,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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try {
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VariantStratifier vs = c.newInstance();
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vs.initialize(jexlExpressions, compNames, knownNames, evalNames, sampleNames);
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vs.initialize(jexlExpressions, compNames, knownNames, evalNames, sampleNamesForStratification);
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strats.add(vs);
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} catch (InstantiationException e) {
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@ -372,15 +374,14 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evalNames);
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Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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// If we're not using the per-sample stratification, don't bother loading the sample list
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if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
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sampleNames.addAll(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
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numSamples = sampleNames.size();
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} else {
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numSamples = vcfSamples.size();
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}
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// Load the sample list
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sampleNamesForEvaluation.addAll(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
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numSamples = sampleNamesForEvaluation.size();
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sampleNames.add(ALL_SAMPLE_NAME);
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if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
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sampleNamesForStratification.addAll(sampleNamesForEvaluation);
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}
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sampleNamesForStratification.add(ALL_SAMPLE_NAME);
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// Initialize select expressions
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jexlExpressions.addAll(VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS));
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@ -411,21 +412,30 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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*
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* @param tracker the reference metadata tracker
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* @param ref the reference context
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* @param compNames the comp track names
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* @param evalNames the evaluation track names
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* @return the set of allowable variation types
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*/
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private EnumSet<VariantContext.Type> getAllowableVariationTypes(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> evalNames) {
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private EnumSet<VariantContext.Type> getAllowableVariationTypes(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> compNames, Set<String> evalNames) {
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EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.NO_VARIATION);
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if (tracker != null) {
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Collection<VariantContext> vcs = tracker.getVariantContexts(ref, evalNames, null, ref.getLocus(), true, false);
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Collection<VariantContext> evalvcs = tracker.getVariantContexts(ref, evalNames, null, ref.getLocus(), true, false);
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for ( VariantContext vc : vcs ) {
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for ( VariantContext vc : evalvcs ) {
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allowableTypes.add(vc.getType());
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}
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} else {
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allowableTypes.add(VariantContext.Type.SNP);
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if (allowableTypes.size() == 1) {
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// We didn't find any variation in the eval track, so now let's look at the comp track for allowable types
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Collection<VariantContext> compvcs = tracker.getVariantContexts(ref, compNames, null, ref.getLocus(), true, false);
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for ( VariantContext vc : compvcs ) {
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allowableTypes.add(vc.getType());
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}
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}
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}
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return allowableTypes;
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}
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@ -478,42 +488,41 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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* @param tracker the metadata tracker
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* @param ref the reference context
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* @param trackNames the list of track names to process
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* @param sampleNames the list of samples to include
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* @param allowableTypes a set of allowable variation types
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* @param byFilter if false, only accept PASSing VariantContexts. Otherwise, accept both PASSing and filtered sites
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* @param trackPerSample if false, don't stratify per sample (and don't cut up the VariantContext like we would need to do this)
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* @param allowNoCalls if false, don't accept no-call loci from a variant track
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* @return a mapping of track names to a list of VariantContext objects
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*/
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private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, Set<String> sampleNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter) {
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private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean trackPerSample, boolean allowNoCalls) {
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HashMap<String, HashMap<String, VariantContext>> bindings = new HashMap<String, HashMap<String, VariantContext>>();
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for ( String trackName : trackNames ) {
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Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, allowableTypes, ref.getLocus(), true, true);
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VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null;
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HashMap<String, VariantContext> vcs = new HashMap<String, VariantContext>();
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Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, allowableTypes, ref.getLocus(), true, true);
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VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null;
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// First, filter the VariantContext to represent only the samples for evaluation
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if ( vc != null ) {
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ArrayList<String> sampleNamesMinusAll = new ArrayList<String>();
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VariantContext vcsub = vc;
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for ( String sampleName : sampleNames ) {
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VariantContext vcsub = vc;
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if (!sampleName.equals(ALL_SAMPLE_NAME)) {
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vcsub = getSubsetOfVariantContext(vc, sampleName);
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sampleNamesMinusAll.add(sampleName);
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}
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if (byFilter || !vcsub.isFiltered()) {
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vcs.put(sampleName, vcsub);
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}
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if (vc.hasGenotypes(sampleNamesForEvaluation)) {
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vcsub = getSubsetOfVariantContext(vc, sampleNamesForEvaluation);
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}
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if ( trackName.contains("eval") ) {
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VariantContext vcsub = (sampleNamesMinusAll.size() > 0) ? getSubsetOfVariantContext(vc, sampleNamesMinusAll) : vc;
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if ((byFilter || !vcsub.isFiltered()) && (allowNoCalls || vcsub.getType() != VariantContext.Type.NO_VARIATION)) {
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vcs.put(ALL_SAMPLE_NAME, vcsub);
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}
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if (byFilter || !vcsub.isFiltered()) {
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vcs.put(ALL_SAMPLE_NAME, vcsub);
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// Now, if stratifying, split the subsetted vc per sample and add each as a new context
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if ( trackPerSample ) {
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for ( String sampleName : sampleNamesForEvaluation ) {
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VariantContext samplevc = getSubsetOfVariantContext(vc, sampleName);
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if ((byFilter || !samplevc.isFiltered()) && (allowNoCalls || samplevc.getType() != VariantContext.Type.NO_VARIATION)) {
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vcs.put(sampleName, samplevc);
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}
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}
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}
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@ -532,35 +541,25 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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* @param ref the reference context
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* @param compNames the list of comp names to process
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* @param evalNames the list of eval names to process
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* @param sampleNames the list of samples to include
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* @return a mapping of track names to a list of VariantContext objects
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*/
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private HashMap<String, HashMap<String, VariantContext>> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> compNames, Set<String> evalNames, Set<String> sampleNames) {
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private HashMap<String, HashMap<String, VariantContext>> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> compNames, Set<String> evalNames) {
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HashMap<String, HashMap<String, VariantContext>> vcs = new HashMap<String, HashMap<String, VariantContext>>();
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Set<String> allSamplesList = new HashSet<String>();
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allSamplesList.add(ALL_SAMPLE_NAME);
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EnumSet<VariantContext.Type> allowableTypes = getAllowableVariationTypes(tracker, ref, compNames, evalNames);
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EnumSet<VariantContext.Type> allowableTypes = getAllowableVariationTypes(tracker, ref, evalNames);
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boolean perSampleIsEnabled = false;
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boolean byFilter = false;
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boolean perSampleIsEnabled = false;
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for (VariantStratifier vs : stratificationObjects) {
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if (vs.getClass().getSimpleName().equals("Sample")) {
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perSampleIsEnabled = true;
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} else if (vs.getClass().getSimpleName().equals("Filter")) {
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if (vs.getClass().getSimpleName().equals("Filter")) {
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byFilter = true;
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} else if (vs.getClass().getSimpleName().equals("Sample")) {
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perSampleIsEnabled = true;
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}
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}
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HashMap<String, HashMap<String, VariantContext>> evalBindings;
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if (perSampleIsEnabled) {
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evalBindings = bindVariantContexts(tracker, ref, evalNames, sampleNames, allowableTypes, byFilter);
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} else {
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evalBindings = bindVariantContexts(tracker, ref, evalNames, allSamplesList, allowableTypes, byFilter);
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}
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HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allSamplesList, allowableTypes, byFilter);
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HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, perSampleIsEnabled, true);
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HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false);
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vcs.putAll(compBindings);
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vcs.putAll(evalBindings);
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@ -657,13 +656,13 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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}
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// track sample vc
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HashMap<String, HashMap<String, VariantContext>> vcs = getVariantContexts(tracker, ref, compNames, evalNames, sampleNames);
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HashMap<String, HashMap<String, VariantContext>> vcs = getVariantContexts(tracker, ref, compNames, evalNames);
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for ( String compName : compNames ) {
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VariantContext comp = vcs.containsKey(compName) && vcs.get(compName) != null && vcs.get(compName).containsKey(ALL_SAMPLE_NAME) ? vcs.get(compName).get(ALL_SAMPLE_NAME) : null;
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for ( String evalName : evalNames ) {
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for ( String sampleName : sampleNames ) {
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for ( String sampleName : sampleNamesForStratification ) {
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VariantContext eval = vcs.containsKey(evalName) && vcs.get(evalName) != null ? vcs.get(evalName).get(sampleName) : null;
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HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
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@ -76,10 +76,13 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
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}
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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boolean expectingIndels = false;
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//boolean expectingIndels = false;
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boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ;
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boolean evalIsGood = expectingIndels ? eval != null && eval.isIndel() : eval != null && eval.isSNP() ;
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//boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ;
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//boolean evalIsGood = expectingIndels ? eval != null && eval.isIndel() : eval != null && eval.isSNP() ;
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boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP() ;
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boolean evalIsGood = eval != null && eval.isSNP() ;
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if (compIsGood) nCompSNPs++; // count the number of comp events
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if (evalIsGood) nEvalSNPs++; // count the number of eval events
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@ -87,8 +90,9 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
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if (compIsGood && evalIsGood) {
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nSNPsAtComp++;
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if (!discordantP(eval, comp)) // count whether we're concordant or not with the comp value
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if (!discordantP(eval, comp)) { // count whether we're concordant or not with the comp value
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nConcordant++;
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}
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}
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return null; // we don't capture any interesting sites
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@ -15,7 +15,6 @@ public class Sample extends VariantStratifier {
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@Override
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public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
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samples = new ArrayList<String>();
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samples.add(VariantEvalWalker.ALL_SAMPLE_NAME);
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samples.addAll(sampleNames);
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}
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@ -52,7 +52,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
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public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
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for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
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//synchronized ( evaluation ) {
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//synchronized ( this ) {
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// we always call update0 in case the evaluation tracks things like number of bases covered
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//evaluation.update0(tracker, ref, context);
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@ -69,9 +69,9 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
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break;
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case 2:
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if (eval != null) {
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//if (eval != null) {
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evaluation.update2(eval, comp, tracker, ref, context);
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}
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//}
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break;
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default:
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@ -82,8 +82,10 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
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}
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public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
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evaluation.update0(tracker, ref, context);
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}
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//synchronized (this) {
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for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
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evaluation.update0(tracker, ref, context);
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}
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//}
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}
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}
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@ -29,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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String extraArgs = "-L 1:1-10,000,000";
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
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1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3"));
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1, Arrays.asList("0087b2a096aa99135b065aa9a0fff34c"));
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//executeTestParallel("testSelect1", spec);
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executeTest("testSelect1", spec);
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}
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@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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for (String vcfFile : vcfFiles) {
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WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
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1,
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Arrays.asList("7a6754176b573d14b6be7c808a04929d"));
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Arrays.asList("bb16335f9510bcab2bd14a4299afd879"));
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//executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
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executeTest("testVEGenotypeConcordance" + vcfFile, spec);
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}
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@ -60,8 +60,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testVESimple() {
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HashMap<String, String> expectations = new HashMap<String, String>();
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expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee");
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expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb");
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expectations.put("-L 1:1-10,000,000", "e46e8e7457b338c4cfec62ee7aa51ffe");
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expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "a0554ca0baa097a1761da3f7e8487833");
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for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
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String extraArgs = entry.getKey();
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@ -84,10 +84,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
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String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b";
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String matchingMD5 = "5050011ad00b859faf2be679830bec90";
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expectations.put("", matchingMD5);
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expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
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expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b");
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expectations.put(" -knownName comp_hapmap", "5050011ad00b859faf2be679830bec90");
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for (String tests : testsEnumerations) {
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for (Map.Entry<String, String> entry : expectations.entrySet()) {
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String extraArgs2 = entry.getKey();
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@ -133,7 +133,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testCompVsEvalAC() {
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String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("929e4ec46fb6957c29803531322bb35e"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("113228ffa35e0f67b8e067860c04171f"));
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//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
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executeTest("testCompVsEvalAC",spec);
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}
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@ -150,6 +150,14 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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executeTest("testTranches",spec);
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}
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@Test
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public void testCompOverlap() {
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String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81377be26bf8fa32339d01c173428f7d"));
|
||||
//executeTestParallel("testTranches",spec);
|
||||
executeTest("testCompOverlap",spec);
|
||||
}
|
||||
|
||||
// @Test
|
||||
// public void testVEValidatePass() {
|
||||
// String extraArgs = "-L 1:1-10,000,000";
|
||||
|
|
|
|||
Loading…
Reference in New Issue