Addition of moltenize argument for moltenized tabular output. NRD/NRS not moltenized because there are only two columns.
This commit is contained in:
Chris Hartl
parent
327169b283
commit
e15d4ad278
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@ -75,22 +75,43 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
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@Argument(fullName="ignoreFilters",doc="Filters will be ignored",required=false)
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@Argument(fullName="ignoreFilters",doc="Filters will be ignored",required=false)
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boolean ignoreFilters = false;
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boolean ignoreFilters = false;
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@Argument(shortName="gfe", fullName="genotypeFilterExpressionEval", doc="One or more criteria to use to set EVAL genotypes to no-call. "+
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"These genotype-level filters are only applied to the EVAL rod.", required=false)
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public ArrayList<String> genotypeFilterExpressionsEval = new ArrayList<String>();
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@Argument(shortName="gfc", fullName="genotypeFilterExpressionComp", doc="One or more criteria to use to set COMP genotypes to no-call. "+
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"These genotype-level filters are only applied to the COMP rod.", required=false)
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public ArrayList<String> genotypeFilterExpressionsComp = new ArrayList<String>();
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@Argument(shortName="moltenize",fullName="moltenize",doc="Molten rather than tabular output")
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public boolean moltenize = false;
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@Output
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@Output
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PrintStream out;
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PrintStream out;
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List<String> evalSamples;
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private List<String> evalSamples;
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List<String> compSamples;
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private List<String> compSamples;
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private List<VariantContextUtils.JexlVCMatchExp> evalJexls = null;
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private List<VariantContextUtils.JexlVCMatchExp> compJexls = null;
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// todo -- deal with occurrences like:
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// Eval: 20 4000 A C
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// Eval: 20 4000 A AC
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// Comp: 20 4000 A C
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// currently this results in a warning and skipping
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// todo -- extend to multiple eval, multiple comp
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// todo -- table with "proportion of overlapping sites" (not just eval/comp margins)
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// todo -- table with "proportion of overlapping sites" (not just eval/comp margins)
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// todo -- genotype-level filtering
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// todo -- moltenize
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public void initialize() {
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evalJexls = initializeJexl(genotypeFilterExpressionsEval);
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compJexls = initializeJexl(genotypeFilterExpressionsComp);
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}
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private List<VariantContextUtils.JexlVCMatchExp> initializeJexl(ArrayList<String> genotypeFilterExpressions) {
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ArrayList<String> dummyNames = new ArrayList<String>(genotypeFilterExpressions.size());
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int expCount = 1;
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for ( String exp : genotypeFilterExpressions ) {
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dummyNames.add(String.format("gfe%d",expCount++));
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}
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return VariantContextUtils.initializeMatchExps(dummyNames, genotypeFilterExpressions);
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}
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public ConcordanceMetrics reduceInit() {
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public ConcordanceMetrics reduceInit() {
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Map<String,VCFHeader> headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding));
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Map<String,VCFHeader> headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding));
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VCFHeader evalHeader = headerMap.get(evalBinding.getName());
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VCFHeader evalHeader = headerMap.get(evalBinding.getName());
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@ -110,15 +131,19 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
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List<VariantContext> eval = tracker.getValues(evalBinding,ref.getLocus());
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List<VariantContext> eval = tracker.getValues(evalBinding,ref.getLocus());
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List<VariantContext> comp = tracker.getValues(compBinding,ref.getLocus());
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List<VariantContext> comp = tracker.getValues(compBinding,ref.getLocus());
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if ( eval.size() > 1 || comp.size() > 1 ) {
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if ( eval.size() > 1 || comp.size() > 1 ) {
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logger.info("Eval or Comp Rod at position " + ref.getLocus().toString() + " has multiple records. Resolving.");
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if ( noDuplicateTypes(eval) && noDuplicateTypes(comp) ) {
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evalCompPair = resolveMultipleRecords(eval,comp);
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logger.info("Eval or Comp Rod at position " + ref.getLocus().toString() + " has multiple records. Resolving.");
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evalCompPair = resolveMultipleRecords(eval,comp);
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} else {
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logger.warn("Eval or Comp Rod at position "+ref.getLocus().toString()+" has multiple records of the same type. This locus will be skipped.");
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}
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} else {
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} else {
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// if a rod is missing, explicitly create a variant context with 'missing' genotypes. Slow, but correct.
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// if a rod is missing, explicitly create a variant context with 'missing' genotypes. Slow, but correct.
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// note that if there is no eval rod there must be a comp rod, and also the reverse
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// note that if there is no eval rod there must be a comp rod, and also the reverse
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VariantContext evalContext = eval.size() == 1 ? eval.get(0) : createEmptyContext(comp.get(0),evalSamples);
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VariantContext evalContext = eval.size() == 1 ? eval.get(0) : createEmptyContext(comp.get(0),evalSamples);
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VariantContext compContext = comp.size() == 1 ? comp.get(0) : createEmptyContext(eval.get(0),compSamples);
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VariantContext compContext = comp.size() == 1 ? comp.get(0) : createEmptyContext(eval.get(0),compSamples);
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evalContext = filterGenotypes(evalContext,ignoreFilters);
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evalContext = filterGenotypes(evalContext,ignoreFilters,evalJexls);
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compContext = filterGenotypes(compContext,ignoreFilters);
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compContext = filterGenotypes(compContext,ignoreFilters,compJexls);
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evalCompPair.add(new Pair<VariantContext, VariantContext>(evalContext,compContext));
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evalCompPair.add(new Pair<VariantContext, VariantContext>(evalContext,compContext));
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}
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}
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}
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}
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@ -126,9 +151,21 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
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return evalCompPair;
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return evalCompPair;
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}
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}
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private boolean noDuplicateTypes(List<VariantContext> vcList) {
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HashSet<VariantContext.Type> types = new HashSet<VariantContext.Type>(vcList.size());
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for ( VariantContext vc : vcList ) {
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VariantContext.Type type = vc.getType();
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if ( types.contains(type) )
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return false;
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types.add(type);
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}
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return true;
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}
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/**
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/**
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* The point of this method is to match up pairs of evals and comps by their alternate alleles. Basically multiple records could
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* The point of this method is to match up pairs of evals and comps by their type (or alternate alleles for mixed).
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* exist for a site such as:
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* Basically multiple records could exist for a site such as:
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* Eval: 20 4000 A C
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* Eval: 20 4000 A C
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* Eval: 20 4000 A AC
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* Eval: 20 4000 A AC
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* Comp: 20 4000 A C
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* Comp: 20 4000 A C
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@ -146,14 +183,19 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
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List<Pair<VariantContext,VariantContext>> resolvedPairs = new ArrayList<Pair<VariantContext,VariantContext>>(evalList.size()+compList.size()); // oversized but w/e
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List<Pair<VariantContext,VariantContext>> resolvedPairs = new ArrayList<Pair<VariantContext,VariantContext>>(evalList.size()+compList.size()); // oversized but w/e
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List<VariantContext> pairedEval = new ArrayList<VariantContext>(evalList.size());
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List<VariantContext> pairedEval = new ArrayList<VariantContext>(evalList.size());
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for ( VariantContext eval : evalList ) {
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for ( VariantContext eval : evalList ) {
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Set<Allele> evalAlts = new HashSet<Allele>(eval.getAlternateAlleles());
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VariantContext.Type evalType = eval.getType();
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Set<Allele> evalAlleles = new HashSet<Allele>(eval.getAlternateAlleles());
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VariantContext pairedComp = null;
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VariantContext pairedComp = null;
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for ( VariantContext comp : compList ) {
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for ( VariantContext comp : compList ) {
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for ( Allele compAlt : comp.getAlternateAlleles() ) {
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if ( evalType.equals(comp.getType()) ) {
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if ( evalAlts.contains(compAlt) ) {
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pairedComp = comp;
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// matching alt allele, pair these records
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break;
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pairedComp = comp;
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} else if ( eval.isMixed() || comp.isMixed() ) {
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break;
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for ( Allele compAllele : comp.getAlternateAlleles() ) {
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if ( evalAlleles.contains(compAllele) ) {
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pairedComp = comp;
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break;
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}
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}
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}
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}
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}
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}
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}
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@ -197,83 +239,202 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
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GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length);
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GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length);
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GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS and NRD",2);
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GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS and NRD",2);
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GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length);
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GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length);
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concordanceCompProportions.addColumn("Sample","%s");
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if ( moltenize ) {
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concordanceCounts.addColumn("Sample","%s");
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concordanceCompProportions.addColumn("Sample","%s");
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concordanceEvalProportions.addColumn("Sample","%s");
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concordanceCounts.addColumn("Sample","%s");
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concordanceSummary.addColumn("Sample","%s");
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concordanceEvalProportions.addColumn("Sample","%s");
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for ( GenotypeType evalType : GenotypeType.values() ) {
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concordanceSummary.addColumn("Sample","%s");
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for ( GenotypeType compType : GenotypeType.values() ) {
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String colKey = String.format("%s_%s", evalType.toString(), compType.toString());
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concordanceCounts.addColumn(colKey,"%d");
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if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
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concordanceEvalProportions.addColumn(colKey,"%.3f");
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if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
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concordanceCompProportions.addColumn(colKey,"%.3f");
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}
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}
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concordanceEvalProportions.addColumn("Mismatching_Alleles","%.3f");
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concordanceCompProportions.addColumn("Mismatching_Alleles","%.3f");
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concordanceCounts.addColumn("Mismatching_Alleles","%d");
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concordanceSummary.addColumn("Non-Reference Sensitivity","%.3f");
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concordanceSummary.addColumn("Non-Reference Discrepancy","%.3f");
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for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
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siteConcordance.addColumn(type.toString(),"%d");
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}
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for ( Map.Entry<String,ConcordanceMetrics.GenotypeConcordanceTable> entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) {
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concordanceCompProportions.addColumn("Eval_Genotype","%s");
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ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue();
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concordanceCounts.addColumn("Eval_Genotype","%s");
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concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey());
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concordanceEvalProportions.addColumn("Eval_Genotype","%s");
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concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey());
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concordanceSummary.addColumn("Non-Reference_Discrepancy","%.3f");
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concordanceCounts.set(entry.getKey(),"Sample",entry.getKey());
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concordanceCompProportions.addColumn("Comp_Genotype","%s");
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concordanceCounts.addColumn("Comp_Genotype","%s");
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concordanceEvalProportions.addColumn("Comp_Genotype","%s");
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concordanceSummary.addColumn("Non-Reference_Sensitivity","%.3f");
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concordanceCompProportions.addColumn("Proportion","%.3f");
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concordanceCounts.addColumn("Count","%d");
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concordanceEvalProportions.addColumn("Proportion","%.3f");
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for ( Map.Entry<String,ConcordanceMetrics.GenotypeConcordanceTable> entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) {
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ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue();
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for ( GenotypeType evalType : GenotypeType.values() ) {
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for ( GenotypeType compType : GenotypeType.values() ) {
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String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString());
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concordanceCounts.set(rowKey,"Sample",entry.getKey());
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concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString());
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int count = table.get(evalType, compType);
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concordanceCounts.set(rowKey,"Count",count);
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if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
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concordanceEvalProportions.set(rowKey,"Sample",entry.getKey());
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concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString());
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concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
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}
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if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
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concordanceCompProportions.set(rowKey,"Sample",entry.getKey());
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concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString());
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concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
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}
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}
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}
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String mismatchKey = String.format("%s_%s",entry.getKey(),"Mismatching");
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concordanceCounts.set(mismatchKey,"Sample",entry.getKey());
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concordanceCounts.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceCounts.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(mismatchKey,"Sample",entry.getKey());
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concordanceEvalProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceCompProportions.set(mismatchKey,"Sample",entry.getKey());
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concordanceCompProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceCompProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
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concordanceCompProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
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concordanceCounts.set(mismatchKey,"Count",table.getnMismatchingAlt());
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}
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String sampleKey = "ALL";
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ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
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for ( GenotypeType evalType : GenotypeType.values() ) {
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for ( GenotypeType compType : GenotypeType.values() ) {
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String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString());
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concordanceCounts.set(rowKey,"Sample",sampleKey);
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concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString());
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int count = table.get(evalType, compType);
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concordanceCounts.set(rowKey,"Count",count);
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if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
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concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
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concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString());
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concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
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}
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if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
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concordanceCompProportions.set(rowKey,"Sample",sampleKey);
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concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
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concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString());
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concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
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}
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}
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}
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String rowKey = String.format("%s_%s",sampleKey,"Mismatching");
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concordanceCounts.set(rowKey,"Sample",sampleKey);
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concordanceCounts.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceCounts.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
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concordanceEvalProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceCompProportions.set(rowKey,"Sample",sampleKey);
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concordanceCompProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
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concordanceCompProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
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concordanceEvalProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
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concordanceCompProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
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concordanceCounts.set(rowKey,"Count",table.getnMismatchingAlt());
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for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
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concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey());
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concordanceSummary.set(nrsEntry.getKey(),"Non-Reference_Sensitivity",nrsEntry.getValue());
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}
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for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
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concordanceSummary.set(nrdEntry.getKey(),"Non-Reference_Discrepancy",nrdEntry.getValue());
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}
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concordanceSummary.set("ALL_NRS_NRD","Sample","ALL");
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concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Sensitivity",metrics.getOverallNRS());
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||||||
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concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Discrepancy",metrics.getOverallNRD());
|
||||||
|
|
||||||
|
|
||||||
|
for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
|
||||||
|
siteConcordance.addColumn(type.toString(),"%d");
|
||||||
|
}
|
||||||
|
|
||||||
|
for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
|
||||||
|
siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type));
|
||||||
|
}
|
||||||
|
|
||||||
|
} else {
|
||||||
|
concordanceCompProportions.addColumn("Sample","%s");
|
||||||
|
concordanceCounts.addColumn("Sample","%s");
|
||||||
|
concordanceEvalProportions.addColumn("Sample","%s");
|
||||||
|
concordanceSummary.addColumn("Sample","%s");
|
||||||
|
for ( GenotypeType evalType : GenotypeType.values() ) {
|
||||||
|
for ( GenotypeType compType : GenotypeType.values() ) {
|
||||||
|
String colKey = String.format("%s_%s", evalType.toString(), compType.toString());
|
||||||
|
concordanceCounts.addColumn(colKey,"%d");
|
||||||
|
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
|
||||||
|
concordanceEvalProportions.addColumn(colKey,"%.3f");
|
||||||
|
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
|
||||||
|
concordanceCompProportions.addColumn(colKey,"%.3f");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
concordanceEvalProportions.addColumn("Mismatching_Alleles","%.3f");
|
||||||
|
concordanceCompProportions.addColumn("Mismatching_Alleles","%.3f");
|
||||||
|
concordanceCounts.addColumn("Mismatching_Alleles","%d");
|
||||||
|
concordanceSummary.addColumn("Non-Reference Sensitivity","%.3f");
|
||||||
|
concordanceSummary.addColumn("Non-Reference Discrepancy","%.3f");
|
||||||
|
for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
|
||||||
|
siteConcordance.addColumn(type.toString(),"%d");
|
||||||
|
}
|
||||||
|
|
||||||
|
for ( Map.Entry<String,ConcordanceMetrics.GenotypeConcordanceTable> entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) {
|
||||||
|
ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue();
|
||||||
|
concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey());
|
||||||
|
concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey());
|
||||||
|
concordanceCounts.set(entry.getKey(),"Sample",entry.getKey());
|
||||||
|
for ( GenotypeType evalType : GenotypeType.values() ) {
|
||||||
|
for ( GenotypeType compType : GenotypeType.values() ) {
|
||||||
|
String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
|
||||||
|
int count = table.get(evalType, compType);
|
||||||
|
concordanceCounts.set(entry.getKey(),colKey,count);
|
||||||
|
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
|
||||||
|
concordanceEvalProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
|
||||||
|
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
|
||||||
|
concordanceCompProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
|
||||||
|
concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
|
||||||
|
concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt());
|
||||||
|
}
|
||||||
|
|
||||||
|
String rowKey = "ALL";
|
||||||
|
concordanceCompProportions.set(rowKey,"Sample",rowKey);
|
||||||
|
concordanceEvalProportions.set(rowKey,"Sample",rowKey);
|
||||||
|
concordanceCounts.set(rowKey,"Sample",rowKey);
|
||||||
|
ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
|
||||||
for ( GenotypeType evalType : GenotypeType.values() ) {
|
for ( GenotypeType evalType : GenotypeType.values() ) {
|
||||||
for ( GenotypeType compType : GenotypeType.values() ) {
|
for ( GenotypeType compType : GenotypeType.values() ) {
|
||||||
String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
|
String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
|
||||||
int count = table.get(evalType, compType);
|
int count = table.get(evalType,compType);
|
||||||
concordanceCounts.set(entry.getKey(),colKey,count);
|
concordanceCounts.set(rowKey,colKey,count);
|
||||||
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
|
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
|
||||||
concordanceEvalProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
|
concordanceEvalProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
|
||||||
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
|
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
|
||||||
concordanceCompProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
|
concordanceCompProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
|
concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
|
||||||
concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
|
concordanceCompProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
|
||||||
concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt());
|
concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt());
|
||||||
}
|
|
||||||
|
|
||||||
String rowKey = "ALL";
|
for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
|
||||||
concordanceCompProportions.set(rowKey,"Sample",rowKey);
|
concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey());
|
||||||
concordanceEvalProportions.set(rowKey,"Sample",rowKey);
|
concordanceSummary.set(nrsEntry.getKey(),"Non-Reference Sensitivity",nrsEntry.getValue());
|
||||||
concordanceCounts.set(rowKey,"Sample",rowKey);
|
|
||||||
ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
|
|
||||||
for ( GenotypeType evalType : GenotypeType.values() ) {
|
|
||||||
for ( GenotypeType compType : GenotypeType.values() ) {
|
|
||||||
String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
|
|
||||||
int count = table.get(evalType,compType);
|
|
||||||
concordanceCounts.set(rowKey,colKey,count);
|
|
||||||
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
|
|
||||||
concordanceEvalProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
|
|
||||||
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
|
|
||||||
concordanceCompProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
|
|
||||||
}
|
}
|
||||||
}
|
for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
|
||||||
concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
|
concordanceSummary.set(nrdEntry.getKey(),"Non-Reference Discrepancy",nrdEntry.getValue());
|
||||||
concordanceCompProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
|
}
|
||||||
concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt());
|
concordanceSummary.set("ALL","Sample","ALL");
|
||||||
|
concordanceSummary.set("ALL","Non-Reference Sensitivity",metrics.getOverallNRS());
|
||||||
|
concordanceSummary.set("ALL","Non-Reference Discrepancy",metrics.getOverallNRD());
|
||||||
|
|
||||||
for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
|
for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
|
||||||
concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey());
|
siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type));
|
||||||
concordanceSummary.set(nrsEntry.getKey(),"Non-Reference Sensitivity",nrsEntry.getValue());
|
}
|
||||||
}
|
|
||||||
for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
|
|
||||||
concordanceSummary.set(nrdEntry.getKey(),"Non-Reference Discrepancy",nrdEntry.getValue());
|
|
||||||
}
|
|
||||||
concordanceSummary.set("ALL","Sample","ALL");
|
|
||||||
concordanceSummary.set("ALL","Non-Reference Sensitivity",metrics.getOverallNRS());
|
|
||||||
concordanceSummary.set("ALL","Non-Reference Discrepancy",metrics.getOverallNRD());
|
|
||||||
|
|
||||||
for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
|
|
||||||
siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type));
|
|
||||||
}
|
}
|
||||||
|
|
||||||
report.addTable(concordanceCompProportions);
|
report.addTable(concordanceCompProportions);
|
||||||
|
|
@ -298,13 +459,32 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
|
||||||
return builder.make();
|
return builder.make();
|
||||||
}
|
}
|
||||||
|
|
||||||
public VariantContext filterGenotypes(VariantContext context, boolean ignoreSiteFilter) {
|
public VariantContext filterGenotypes(VariantContext context, boolean ignoreSiteFilter, List<VariantContextUtils.JexlVCMatchExp> exps) {
|
||||||
// placeholder method for genotype-level filtering. However if the site itself is filtered,
|
// placeholder method for genotype-level filtering. However if the site itself is filtered,
|
||||||
// and such filters are not ignored, the genotype-level data should be altered to reflect this
|
// and such filters are not ignored, the genotype-level data should be altered to reflect this
|
||||||
|
|
||||||
if ( ! context.isFiltered() || ignoreSiteFilter ) {
|
if ( ! context.isFiltered() || ignoreSiteFilter ) {
|
||||||
// todo -- add genotype-level jexl filtering here
|
List<Genotype> filteredGenotypes = new ArrayList<Genotype>(context.getNSamples());
|
||||||
return context;
|
for ( Genotype g : context.getGenotypes() ) {
|
||||||
|
Map<VariantContextUtils.JexlVCMatchExp, Boolean> matchMap = VariantContextUtils.match(context, g, exps);
|
||||||
|
boolean filtered = false;
|
||||||
|
for ( Boolean b : matchMap.values() ) {
|
||||||
|
if ( b ) {
|
||||||
|
filtered = true;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if ( filtered ) {
|
||||||
|
filteredGenotypes.add(GenotypeBuilder.create(g.getSampleName(),Arrays.asList(Allele.NO_CALL,Allele.NO_CALL),g.getExtendedAttributes()));
|
||||||
|
} else {
|
||||||
|
filteredGenotypes.add(g);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
VariantContextBuilder builder = new VariantContextBuilder(context);
|
||||||
|
builder.genotypes(filteredGenotypes);
|
||||||
|
return builder.make();
|
||||||
}
|
}
|
||||||
|
|
||||||
VariantContextBuilder builder = new VariantContextBuilder();
|
VariantContextBuilder builder = new VariantContextBuilder();
|
||||||
builder.alleles(Arrays.asList(context.getReference()));
|
builder.alleles(Arrays.asList(context.getReference()));
|
||||||
builder.loc(context.getChr(),context.getStart(),context.getEnd());
|
builder.loc(context.getChr(),context.getStart(),context.getEnd());
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue