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(",")));
public void writeVariant(MongoDBVariantStageConverterTask converterTask, MongoDBVariantStageLoader loader, String variantStr) { Variant variant = new Variant(variantStr); variant.setNames(Collections.emptyList()); StudyEntry studyEntry = new StudyEntry("1", "1"); studyEntry.setFormat(Collections.emptyList()); variant.addStudyEntry(studyEntry); variantMap.put(variant.getChromosome(), variant); loader.write(converterTask.apply(Collections.singletonList(variant))); }
variant.setNames(names); variant.setChromosome(chromosome); variant.setStart(start);
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); // } }