@Test
public void testVcfHtsExportMultiFile() throws Exception {
Query query = new Query();
query.append(VariantQueryParam.STUDY.key(), STUDY_NAME);
Path outputVcf = getTmpRootDir().resolve("hts_mf_" + EXPORTED_FILE_NAME);
int failedVariants = export(outputVcf, query, new QueryOptions(QueryOptions.SORT, true));
assertEquals(0, failedVariants);
Path originalVcf = Paths.get(getResourceUri("filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
VariantReader variantReader = new VariantVcfHtsjdkReader(
originalVcf,
getMetadata(originalVcf),
VARIANT_NORMALIZER);
variantReader.open();
variantReader.pre();
Region region = new Region("22", 16000000);
int batchSize = 2000;
while (checkExportedVCF(originalVcf, variantReader, outputVcf, region, batchSize) != batchSize) {
region = new Region("22", region.getEnd());
}
variantReader.post();
variantReader.close();
}