use of com.google.cloud.genomics.dataflow.utils.GenomicsOptions in project gatk by broadinstitute.
the class ReferenceAPISourceUnitTest method testDummy.
@Test(groups = "cloud")
public void testDummy() {
String referenceName = HS37D5_REF_ID;
final String expected = "AAACAGGTTA";
// -1 because we're using closed intervals
SimpleInterval interval = new SimpleInterval("1", 50001, 50001 + expected.length() - 1);
Logger logger = LogManager.getLogger(ReferenceAPISourceUnitTest.class);
GenomicsOptions options = PipelineOptionsFactory.create().as(GenomicsOptions.class);
options.setApiKey(getGCPTestApiKey());
options.setProject(getGCPTestProject());
// We don't use GATKTestPipeline because we need specific options.
final Pipeline p = TestPipeline.create(options);
ReferenceAPISource refAPISource = makeReferenceAPISource(referenceName, p);
ReferenceBases bases = refAPISource.getReferenceBases(p.getOptions(), interval);
final String actual = new String(bases.getBases());
Assert.assertEquals(actual, expected, "Wrong bases returned");
p.run();
}
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