/** * Remove a cohort (from cohort ID) of a given variant study metadata (from study ID). * * @param cohortId Cohort ID * @param studyId Study ID */ public void removeCohort(String cohortId, String studyId) { // Sanity check if (StringUtils.isEmpty(cohortId)) { logger.error("Cohort ID {} is null or empty.", cohortId); return; } VariantStudyMetadata variantStudyMetadata = getVariantStudyMetadata(studyId); if (variantStudyMetadata == null) { logger.error("Study not found. Check your study ID: '{}'", studyId); return; } if (variantStudyMetadata.getCohorts() != null) { for (int i = 0; i < variantStudyMetadata.getCohorts().size(); i++) { if (cohortId.equals(variantStudyMetadata.getCohorts().get(i).getId())) { variantStudyMetadata.getCohorts().remove(i); return; } } } }
/** * Print to the standard output a summary of the variant metadata manager. * * @throws IOException IOException */ public void printSummary() { StringBuilder res = new StringBuilder(); res.append("Num. studies: ").append(variantMetadata.getStudies().size()).append("\n"); int counter, studyCounter = 0; for (VariantStudyMetadata study: variantMetadata.getStudies()) { studyCounter++; res.append("\tStudy #").append(studyCounter).append(": ").append(study.getId()).append("\n"); res.append("\tNum. files: ").append(study.getFiles().size()).append("\n"); counter = 0; for (VariantFileMetadata file: study.getFiles()) { counter++; res.append("\t\tFile #").append(counter).append(": ").append(file.getId()); res.append(" (").append(file.getSampleIds().size()).append(" samples)\n"); } res.append("\tNum. cohorts: ").append(study.getCohorts().size()).append("\n"); counter = 0; for (Cohort cohort: study.getCohorts()) { counter++; res.append("\t\tCohort #").append(counter).append(": ").append(cohort.getId()); res.append(" (").append(cohort.getSampleIds().size()).append(" samples)\n"); } } System.out.println(res.toString()); }
/** * Add a cohort to a given variant study metadata (from study ID). * * @param cohort Cohort to add * @param studyId Study ID */ public void addCohort(Cohort cohort, String studyId) { // Sanity check if (cohort == null || StringUtils.isEmpty(cohort.getId())) { logger.error("Cohort (or its ID) is null or empty."); return; } VariantStudyMetadata variantStudyMetadata = getVariantStudyMetadata(studyId); if (variantStudyMetadata == null) { logger.error("Study not found. Check your study ID: '{}'", studyId); return; } if (variantStudyMetadata.getCohorts() == null) { variantStudyMetadata.setCohorts(new ArrayList<>()); } for (Cohort coho: variantStudyMetadata.getCohorts()) { if (coho.getId() != null && coho.getId().equals(cohort.getId())) { logger.error("Cohort with id '{}' already exists in study '{}'", cohort.getId(), studyId); return; } } variantStudyMetadata.getCohorts().add(cohort); }
for (Cohort cohort : variantStudyMetadata.getCohorts()) { cohort.setSampleIds(Collections.emptyList());
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; }
vcfHeader.addMetaDataLine(new VCFFilterHeaderLine(VCFConstants.PASSES_FILTERS_v4, "All filters passed")); for (Cohort cohort : variantStudyMetadata.getCohorts()) { String cohortName = cohort.getId(); if (cohortName.equals(StudyEntry.DEFAULT_COHORT)) {