close StorageAPIAvroReader appropriately

[kcibul]

When running with multiple table (ie _001, _002) this would show up in the logs due to the bigquery client not being closed. It didn't cause any harm, but is alarming! Closing the ranges-based readers appropriately now.

Nov 23, 2021 5:45:53 AM io.grpc.internal.ManagedChannelOrphanWrapper$ManagedChannelReference cleanQueue
SEVERE: *~*~*~ Channel ManagedChannelImpl{logId=121, target=bigquerystorage.googleapis.com:443} was not shutdown properly!!! ~*~*~*
    Make sure to call shutdown()/shutdownNow() and wait until awaitTermination() returns true.
java.lang.RuntimeException: ManagedChannel allocation site
	at io.grpc.internal.ManagedChannelOrphanWrapper$ManagedChannelReference.<init>(ManagedChannelOrphanWrapper.java:93)
	at io.grpc.internal.ManagedChannelOrphanWrapper.<init>(ManagedChannelOrphanWrapper.java:53)
	at io.grpc.internal.ManagedChannelOrphanWrapper.<init>(ManagedChannelOrphanWrapper.java:44)
	at io.grpc.internal.ManagedChannelImplBuilder.build(ManagedChannelImplBuilder.java:615)
	at io.grpc.internal.AbstractManagedChannelImplBuilder.build(AbstractManagedChannelImplBuilder.java:261)
	at com.google.api.gax.grpc.InstantiatingGrpcChannelProvider.createSingleChannel(InstantiatingGrpcChannelProvider.java:360)
	at com.google.api.gax.grpc.InstantiatingGrpcChannelProvider.access$1800(InstantiatingGrpcChannelProvider.java:81)
	at com.google.api.gax.grpc.InstantiatingGrpcChannelProvider$1.createSingleChannel(InstantiatingGrpcChannelProvider.java:231)
	at com.google.api.gax.grpc.ChannelPool.create(ChannelPool.java:72)
	at com.google.api.gax.grpc.InstantiatingGrpcChannelProvider.createChannel(InstantiatingGrpcChannelProvider.java:241)
	at com.google.api.gax.grpc.InstantiatingGrpcChannelProvider.getTransportChannel(InstantiatingGrpcChannelProvider.java:219)
	at com.google.api.gax.rpc.ClientContext.create(ClientContext.java:199)
	at com.google.cloud.bigquery.storage.v1.stub.EnhancedBigQueryReadStub.create(EnhancedBigQueryReadStub.java:89)
	at com.google.cloud.bigquery.storage.v1.BigQueryReadClient.<init>(BigQueryReadClient.java:129)
	at com.google.cloud.bigquery.storage.v1.BigQueryReadClient.create(BigQueryReadClient.java:110)
	at com.google.cloud.bigquery.storage.v1.BigQueryReadClient.create(BigQueryReadClient.java:102)
	at org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader.<init>(StorageAPIAvroReader.java:60)
	at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createSortedReferenceRangeCollectionFromBigQuery(ExtractCohortEngine.java:851)
	at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.createVariantsFromUnsortedBigQueryRanges(ExtractCohortEngine.java:891)
	at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohortEngine.traverse(ExtractCohortEngine.java:224)
	at org.broadinstitute.hellbender.tools.gvs.extract.ExtractCohort.traverse(ExtractCohort.java:335)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)

[rsasch]

thanks for the quick fix 👍🏻 (assuming tests pass)