private static FileEntry getFileEntry(Variant variant, String studyId, String fileId) { StudyEntry studyEntry = getStudyEntry(variant, studyId); if (studyEntry == null) { return null; } if (fileId == null) { if (studyEntry.getFiles().size() != 1) { throw new IllegalArgumentException("Required one File per variant. Found " + studyEntry.getFiles().size() + " files instead"); } return studyEntry.getFiles().get(0); } else { return studyEntry.getFile(fileId); } } }
@Override protected FileEntry featureValueOf(StudyEntry actual) { return actual.getFile(fileId); } };
public void addAttribute(String fileId, String key, String value) { getFile(fileId).getAttributes().put(key, value); }
public void addAttributes(String fileId, Map<String, String> attributes) { getFile(fileId).getAttributes().putAll(attributes); }
public static Matcher<StudyEntry> withFileId(String fileId) { return matcher(studyEntry -> studyEntry.getFile(fileId) != null, "with fileId " + fileId); }
String call = studyEntry.getFile(Integer.toString(fileId)).getCall(); if (call != null && !call.isEmpty()) { int indexOf = call.lastIndexOf(":");
@Test public void testIncludeFiles() throws Exception { query = new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_FILE.key(), file12877); queryResult = query(query, options); assertEquals(dbAdaptor.count(null).first().intValue(), queryResult.getNumResults()); for (Variant variant : queryResult.getResult()) { assertTrue(variant.getStudies().size() <= 1); StudyEntry s_1 = variant.getStudy("S_1"); if (s_1 != null) { assertTrue(s_1.getFiles().size() <= 1); if (s_1.getFiles().size() == 1) { assertNotNull(s_1.getFile(file12877)); } } assertTrue(variant.getStudies().size() <= 1); } assertThat(queryResult, everyResult(allOf(not(withStudy("S_2")), not(withStudy("S_3")), not(withStudy("S_4"))))); }
protected void parseInfo(Variant variant, String fileId, String studyId, String info) { StudyEntry study = variant.getStudy(studyId); FileEntry file = study.getFile(fileId);
public static Variant addAttribute(Variant var, String key, String value) { var.getStudy("1").getFile("1").getAttributes().put(key, value); return var; }
List<FileEntry> fileEntries = new ArrayList<>(files.size()); for (String fileId : files) { FileEntry fileEntry = study.getFile(fileId); if (fileEntry == null) {
fileId = 2; studyEntry = new StudyEntry(fileId.toString(), studyId.toString()); FileEntry fileEntry = studyEntry.getFile(fileId.toString()); fileEntry.getAttributes().put("QUAL", "0.01"); fileEntry.getAttributes().put("AN", "2");