private List<String> getFormatOrder(StudyEntry file) { return Lists.newArrayList(file.getFormatAsString().split(":")); }
public static String getJoinedSampleFields(StudyEntry file, String sampleName) { Map<String, String> data = file.getSampleDataAsMap(sampleName); if (data == null) { return ""; } StringBuilder info = new StringBuilder(); for (String formatField : file.getFormatAsString().split(":")) { info.append(data.get(formatField)).append(":"); } return info.toString().isEmpty() ? "." : info.toString(); }
String formatAsString; if (includeAllFormats) { formatAsString = studyEntry.getFormatAsString(); } else { formatAsString = studyEntry.getFormat()
@Test public void testIncludeFormat() { Variant variant = query(new Query(INCLUDE_FORMAT.key(), "GT"), new QueryOptions(QueryOptions.LIMIT, 1)).first(); System.out.println("variant.toJson() = " + variant.toJson()); assertEquals("GT", variant.getStudies().get(0).getFormatAsString()); variant = query(new Query(INCLUDE_FORMAT.key(), "GL"), new QueryOptions(QueryOptions.LIMIT, 1)).first(); System.out.println("variant.toJson() = " + variant.toJson()); assertEquals("GL", variant.getStudies().get(0).getFormatAsString()); variant = query(new Query(INCLUDE_FORMAT.key(), "GT,GL,DS"), new QueryOptions(QueryOptions.LIMIT, 1)).first(); System.out.println("variant.toJson() = " + variant.toJson()); assertEquals("GT:GL:DS", variant.getStudies().get(0).getFormatAsString()); variant = query(new Query(INCLUDE_FORMAT.key(), "GT,XX,GL"), new QueryOptions(QueryOptions.LIMIT, 1)).first(); System.out.println("variant.toJson() = " + variant.toJson()); assertEquals("GT:XX:GL", variant.getStudies().get(0).getFormatAsString()); }
@Test public void indexWithoutOtherFields() throws Exception { StudyConfiguration studyConfiguration = newStudyConfiguration(); runDefaultETL(smallInputUri, getVariantStorageEngine(), studyConfiguration, new ObjectMap(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS.key(), VariantQueryUtils.NONE) .append(VariantStorageEngine.Options.TRANSFORM_FORMAT.key(), "avro") .append(VariantStorageEngine.Options.ANNOTATE.key(), false) .append(VariantStorageEngine.Options.CALCULATE_STATS.key(), false) ); for (Variant variant : variantStorageEngine.getDBAdaptor()) { assertEquals("GT", variant.getStudy(STUDY_NAME).getFormatAsString()); } }