public static Matcher<Variant> overlaps(Region region) { return overlaps(region, true); }
@Test public void testDuplicatedVariantOnlyOneFile_mergeAtSameTime() throws StorageEngineException { List<Variant> file2Variants = createFile2Variants(); List<Variant> file3Variants = createFile3Variants(); file3Variants.add(file3Variants.get(0)); assertThat(file3Variants.get(0), VariantMatchers.overlaps(file2Variants.get(0))); stageVariants(studyConfiguration2, file3Variants, fileId3); stageVariants(studyConfiguration2, file2Variants, fileId2); MongoDBVariantWriteResult result = mergeVariants(studyConfiguration2, Arrays.asList(fileId2, fileId3), null, Collections.emptyList()); assertEqualsResult(new MongoDBVariantWriteResult(4, 0, 0, 0, 0, 2), result); }
public static Matcher<Variant> overlaps(Variant variant) { return overlaps(new Region(variant.getChromosome(), variant.getStart(), variant.getEnd()), true); }
@Test public void testDuplicatedVariantOnlyOneFile_mergeDuplicatedFirst() throws StorageEngineException { List<Variant> file2Variants = createFile2Variants(); List<Variant> file3Variants = createFile3Variants(); file3Variants.add(file3Variants.get(0)); assertThat(file3Variants.get(0), VariantMatchers.overlaps(file2Variants.get(0))); stageVariants(studyConfiguration2, file3Variants, fileId3); stageVariants(studyConfiguration2, file2Variants, fileId2); MongoDBVariantWriteResult resultMergeFile3 = mergeVariants(studyConfiguration2, fileId3, null); MongoDBVariantWriteResult resultMergeFile2 = mergeVariants(studyConfiguration2, fileId2, null); assertEqualsResult(new MongoDBVariantWriteResult(2, 0, 0, 0, 0, 2), resultMergeFile3); assertEqualsResult(new MongoDBVariantWriteResult(2, 0, 2, 0, 0, 0), resultMergeFile2); }
@Test public void testDuplicatedVariantOnlyOneFile_mergeDuplicatedLast() throws StorageEngineException { List<Variant> file2Variants = createFile2Variants(); List<Variant> file3Variants = createFile3Variants(); file3Variants.add(file3Variants.get(0)); assertThat(file3Variants.get(0), VariantMatchers.overlaps(file2Variants.get(0))); stageVariants(studyConfiguration2, file3Variants, fileId3); stageVariants(studyConfiguration2, file2Variants, fileId2); MongoDBVariantWriteResult resultMergeFile2 = mergeVariants(studyConfiguration2, fileId2, null); MongoDBVariantWriteResult resultMergeFile3 = mergeVariants(studyConfiguration2, fileId3, null); assertEqualsResult(new MongoDBVariantWriteResult(2, 0, 0, 0, 0, 0), resultMergeFile2); assertEqualsResult(new MongoDBVariantWriteResult(2, 0, 2, 0, 0, 2), resultMergeFile3); }
public void checkRegion(Region queryRegion, Region overlappingRegion) { queryResult = query(new Query(REGION.key(), queryRegion), null); assertThat(queryResult, everyResult(allVariants, overlaps(overlappingRegion))); }
public void testGetBySampleNameMultiRegion(String expectedSource, QueryOptions options) throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.SAMPLE.key(), "NA12877") .append(VariantQueryParam.REGION.key(), "1:1-12783,M"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", containsString("1"))))))); }
public void testGetByGenotypeMultiRegion(String expectedSource, QueryOptions options) throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.GENOTYPE.key(), "NA12877:1/1") .append(VariantQueryParam.REGION.key(), "1:1-12783,M"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", is("1/1"))))))); }