public static <W extends BoundedWindow> TriggerTester<Integer, Iterable<Integer>, W> nonCombining(
WindowingStrategy<?, W> windowingStrategy) throws Exception {
return new TriggerTester<Integer, Iterable<Integer>, W>(
windowingStrategy,
SystemReduceFn.<String, Integer, W>buffering(VarIntCoder.of()).create(KEY),
IterableCoder.of(VarIntCoder.of()));
}
@Test(dataProvider = "bases")
public void addContextDataTest(
List<GATKRead> reads,
List<Variant> variantList,
List<KV<GATKRead, ReferenceBases>> kvReadRefBases,
List<KV<GATKRead, ReadContextData>> kvReadContextData,
List<SimpleInterval> intervals,
List<KV<GATKRead, Iterable<Variant>>> kvReadiVariant) {
Pipeline p = GATKTestPipeline.create();
DataflowUtils.registerGATKCoders(p);
PCollection<GATKRead> pReads =
DataflowTestUtils.pCollectionCreateAndVerify(p, reads, new GATKReadCoder());
PCollection<KV<GATKRead, ReferenceBases>> pReadRef =
DataflowTestUtils.pCollectionCreateAndVerify(
p,
kvReadRefBases,
KvCoder.of(new GATKReadCoder(), SerializableCoder.of(ReferenceBases.class)));
PCollection<KV<GATKRead, Iterable<Variant>>> pReadVariants =
p.apply(
Create.of(kvReadiVariant)
.withCoder(KvCoder.of(new GATKReadCoder(), IterableCoder.of(new VariantCoder()))));
PCollection<KV<GATKRead, ReadContextData>> joinedResults =
AddContextDataToRead.join(pReads, pReadRef, pReadVariants);
PCollection<KV<GATKRead, ReadContextData>> pkvReadContextData =
p.apply(
Create.of(kvReadContextData)
.withCoder(KvCoder.of(new GATKReadCoder(), new ReadContextDataCoder())));
DataflowTestUtils.keyReadContextDataMatcher(joinedResults, pkvReadContextData);
p.run();
}