studyEntryMap.put(studyId, entry); }); variant.setStudies(studies);
variant.addStudyEntry(studyEntry); } else { variant.setStudies(null);
variant.setAlternate(alternateAllele); variant.setId(id); variant.setStudies(studyEntryList); variant.setStrand(strand); variant.setType(VariantType.valueOf(variantType));
public static Variant getVariant(String var) { Variant v = new Variant(var); StudyEntry sb = new StudyEntry("1", "1"); String call = v.getStart() + ":" + v.getReference() + ":" + v.getAlternate() + ":" + 0; sb.setFiles(Collections.singletonList(new FileEntry("1", "", new HashMap<>()))); v.setStudies(Collections.singletonList(sb)); if (v.getAlternate().contains(",")) { String[] alternates = v.getAlternate().split(","); v.setAlternate(alternates[0]); for (int i = 1; i < alternates.length; i++) { v.getStudies().get(0).getSecondaryAlternates().add(new AlternateCoordinate(null, null, null, null, alternates[i], null)); } } return v; }
@Test public void testConvertToDataModelTypeWithoutFiles() { DocumentToVariantConverter converter = new DocumentToVariantConverter(); Variant converted = converter.convertToDataModelType(mongoVariant); variant.setStudies(Collections.<StudyEntry>emptyList()); assertEquals("\n" + variant.toJson() + "\n" + converted.toJson(), variant, converted); }
StudyEntry se = new StudyEntry("1"); se.setFiles(Collections.singletonList(new FileEntry("1", "", new HashMap<>()))); v1.setStudies(Collections.singletonList(se)); se.setFormat(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY)); se.setSamplesPosition(asMap("S1", 0)); se = new StudyEntry("1"); se.setFiles(Collections.singletonList(new FileEntry("1", "", new HashMap<>()))); v2.setStudies(Collections.singletonList(se)); se.setSamplesPosition(asMap("S1", 0)); se.setFormat(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
normalizedVariant.setStudies(Collections.singletonList(studyEntry));
private Variant createVariantSecAlt(String varString, String secAlt) { Variant secAltVar = new Variant(secAlt); Variant variant = new Variant(varString); StudyEntry se = new StudyEntry("1"); AlternateCoordinate ac = new AlternateCoordinate( secAltVar.getChromosome(), secAltVar.getStart(), secAltVar.getEnd(), secAltVar.getReference(), secAltVar.getAlternate(), secAltVar.getType()); se.setSecondaryAlternates(Collections.singletonList(ac)); variant.setStudies(Collections.singletonList(se)); return variant; }
studyEntry.setStudyId(STUDY_NAME); studyEntry.getFiles().get(0).setFileId(fileId); variant.setStudies(Collections.singletonList(studyEntry));