Example 6 with ReferenceAPISource
use of org.broadinstitute.hellbender.engine.datasources.ReferenceAPISource in project gatk by broadinstitute.
the class ReferenceAPISourceUnitTest method queryReferenceAPI.
private ReferenceBases queryReferenceAPI(final String referenceName, final SimpleInterval interval) {
final Pipeline p = setupPipeline();
ReferenceAPISource refAPISource = makeReferenceAPISource(referenceName, p);
return refAPISource.getReferenceBases(p.getOptions(), interval);
}
Also used :
ReferenceAPISource(org.broadinstitute.hellbender.engine.datasources.ReferenceAPISource)
TestPipeline(com.google.cloud.dataflow.sdk.testing.TestPipeline)
Pipeline(com.google.cloud.dataflow.sdk.Pipeline)
Aggregations
ReferenceAPISource (org.broadinstitute.hellbender.engine.datasources.ReferenceAPISource)6
Pipeline (com.google.cloud.dataflow.sdk.Pipeline)5
TestPipeline (com.google.cloud.dataflow.sdk.testing.TestPipeline)5
BaseTest (org.broadinstitute.hellbender.utils.test.BaseTest)4
Test (org.testng.annotations.Test)4
GenomicsOptions (com.google.cloud.genomics.dataflow.utils.GenomicsOptions)1
SAMSequenceDictionary (htsjdk.samtools.SAMSequenceDictionary)1
Logger (org.apache.logging.log4j.Logger)1
SimpleInterval (org.broadinstitute.hellbender.utils.SimpleInterval)1
ReferenceBases (org.broadinstitute.hellbender.utils.reference.ReferenceBases)1
