@Deprecated public static int htsExport(VariantDBIterator iterator, StudyConfiguration studyConfiguration, OutputStream outputStream, Query query, QueryOptions queryOptions) { VariantVcfDataWriter exporter = new VariantVcfDataWriter(studyConfiguration, outputStream, query, queryOptions); exporter.open(); exporter.pre(); iterator.forEachRemaining(exporter::write); exporter.post(); exporter.close(); return exporter.failedVariants; }
@Test public void adjustedVariantStart_SecAlt_INDEL() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Integer adjustStart = dw.adjustedVariantStart(createVariantSecAlt("1:123:A:C", "1:122:GG:-")).getLeft(); assertEquals("Adjusted start position wrong", Integer.valueOf(121), adjustStart); }
@Test public void adjustedVariantStart_SecAlt_MNV() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Integer adjustStart = dw.adjustedVariantStart(createVariantSecAlt("1:123:A:C", "1:122:GG:CC")).getLeft(); assertEquals("Adjusted start position wrong", Integer.valueOf(122), adjustStart); }
@Test public void buildAlleles_SecAlt_INDEL() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Variant variant = createVariantSecAlt("1:123:A:C", "1:122:GGT:-"); List<String> alles = dw.buildAlleles(variant, new ImmutablePair<>(121, 124)); assertEquals("Missing alleles", 3, alles.size()); assertEquals("Ref allele not correctly adjusted", "NNAN", alles.get(0)); assertEquals("Ref allele not correctly adjusted", "NNCN", alles.get(1)); assertEquals("Ref allele not correctly adjusted", "N", alles.get(2)); }
@Test public void buildAlleles_SecAlt_MNV() throws Exception { StudyConfiguration sc = new StudyConfiguration(1, "1"); VariantVcfDataWriter dw = new VariantVcfDataWriter(sc, null, null, null); Variant variant = createVariantSecAlt("1:123:A:C", "1:122:GG:TT"); List<String> alles = dw.buildAlleles(variant, new ImmutablePair<>(122, 123)); assertEquals("Missing alleles", 3, alles.size()); assertEquals("Ref allele not correctly adjusted", "NA", alles.get(0)); assertEquals("Ref allele not correctly adjusted", "NC", alles.get(1)); assertEquals("Ref allele not correctly adjusted", "TT", alles.get(2)); }