protected Variant convert(Variant variant, Map<Integer, StudyEntry> studies, VariantAnnotation annotation) { for (StudyEntry studyEntry : studies.values()) { variant.addStudyEntry(studyEntry); } variant.setAnnotation(annotation); if (annotation != null && StringUtils.isNotEmpty(annotation.getId())) { variant.setId(annotation.getId()); } else { variant.setId(variant.toString()); } if (failOnEmptyVariants && variant.getStudies().isEmpty()) { throw new IllegalStateException("No Studies registered for variant!!! " + variant); } return variant; }
mustSearchVariation.get(i).setId(cacheVariant.getId()); if (mustSearchVariation.get(i).getAnnotation() == null) { mustSearchVariation.get(i).setAnnotation(new VariantAnnotation());
mustSearchVariation.get(i).setId(cacheVariant.getId()); if (mustSearchVariation.get(i).getAnnotation() == null) { mustSearchVariation.get(i).setAnnotation(new VariantAnnotation());
variant.setId(fields[ACCESSION_COLUMN]); if (org.apache.commons.lang3.StringUtils.isNotBlank(fields[SUPPORTING_VARIANTS_COLUMN])) { variant.setNames(Arrays.asList(fields[SUPPORTING_VARIANTS_COLUMN].split(",")));
variant.setId(variantSearchModel.getVariantId());
variant.setId(id); variant.setNames(names); variant.setChromosome(chromosome);
variant.setId(id); variant.setStudies(studyEntryList); variant.setStrand(strand);
Variant expected = merger.merge(variant, variants2.stream().filter(v -> v.toString().equals(variant.toString())).collect(Collectors.toList())); if (expected.getId() == null) { expected.setId(expected.toString());
private Variant newVariant(Variant variant, VariantKeyFields keyFields, StructuralVariation sv) { Variant normalizedVariant = new Variant(variant.getChromosome(), keyFields.getStart(), keyFields.getEnd(), keyFields.getReference(), keyFields.getAlternate()) .setId(variant.getId()) .setNames(variant.getNames()) .setStrand(variant.getStrand()); if (sv != null) { if (normalizedVariant.getSv() != null) { // CI positions may change during the normalization. Update them. normalizedVariant.getSv().setCiStartLeft(sv.getCiStartLeft()); normalizedVariant.getSv().setCiStartRight(sv.getCiStartRight()); normalizedVariant.getSv().setCiEndLeft(sv.getCiEndLeft()); normalizedVariant.getSv().setCiEndRight(sv.getCiEndRight()); } else { normalizedVariant.setSv(sv); } // Variant will never have CopyNumber, because the Alternate is normalized from <CNxx> to <CNV> normalizedVariant.getSv().setCopyNumber(keyFields.getCopyNumber()); normalizedVariant.getSv().setType(VariantBuilder.getCNVSubtype(keyFields.getCopyNumber())); } return normalizedVariant; // normalizedVariant.setAnnotation(variant.getAnnotation()); // if (isSymbolic(variant)) { // StructuralVariation sv = getStructuralVariation(normalizedVariant, keyFields, null); // normalizedVariant.setSv(sv); // } }