/** * Calculate global statistics for the whole study. i.e. cohort ALL * @param metadata VariantStudyMetadata */ public VariantSetStatsCalculator(VariantStudyMetadata metadata) { this.studyId = metadata.getId(); this.metadata = metadata; files = metadata.getFiles() .stream() .map(org.opencb.biodata.models.variant.metadata.VariantFileMetadata::getId) .collect(Collectors.toSet()); samples = metadata.getFiles() .stream() .flatMap(fileMetadata -> fileMetadata.getSampleIds().stream()) .collect(Collectors.toSet()); header = metadata.getAggregatedHeader(); stats = new VariantSetStats(); if (metadata.getStats() == null) { metadata.setStats(new VariantStudyStats(new HashMap<>(), new HashMap<>())); } if (metadata.getStats().getCohortStats() == null) { metadata.getStats().setCohortStats(new HashMap<>()); } metadata.getStats().getCohortStats().put(StudyEntry.DEFAULT_COHORT, stats.getImpl()); }
public List<StudyConfiguration> toStudyConfigurations(VariantMetadata variantMetadata) { List<StudyConfiguration> studyConfigurations = new ArrayList<>(variantMetadata.getStudies().size()); int id = 1; VariantMetadataManager metadataManager = new VariantMetadataManager().setVariantMetadata(variantMetadata); for (VariantStudyMetadata studyMetadata : variantMetadata.getStudies()) { StudyConfiguration sc = new StudyConfiguration(id++, studyMetadata.getId()); studyConfigurations.add(sc); List<Sample> samples = metadataManager.getSamples(studyMetadata.getId()); for (Sample sample : samples) { sc.getSampleIds().put(sample.getId(), id++); } for (VariantFileMetadata fileMetadata : studyMetadata.getFiles()) { int fileId = id++; sc.getIndexedFiles().add(fileId); sc.getFileIds().put(fileMetadata.getPath(), fileId); List<Integer> sampleIds = toSampleIds(sc, fileMetadata.getSampleIds()); sc.getSamplesInFiles().put(fileId, new LinkedHashSet<>(sampleIds)); } for (Cohort cohort : studyMetadata.getCohorts()) { int cohortId = id++; sc.getCohortIds().put(cohort.getId(), cohortId); sc.getCalculatedStats().add(cohortId); sc.getCohorts().put(cohortId, new HashSet<>(toSampleIds(sc, cohort.getSampleIds()))); } sc.setVariantHeader(studyMetadata.getAggregatedHeader()); sc.setAggregation(studyMetadata.getAggregation()); studyMetadata.getAttributes().forEach(sc.getAttributes()::put); } return studyConfigurations; }
public VCFHeader convert(VariantStudyMetadata variantStudyMetadata, List<String> annotations) { VariantFileHeader header = variantStudyMetadata.getAggregatedHeader(); if (header == null) { if (variantStudyMetadata.getFiles() != null && variantStudyMetadata.getFiles().size() == 1) {