diff --git a/.dockstore.yml b/.dockstore.yml index 73592f1ab15..854b0fccdb2 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -227,6 +227,7 @@ workflows: branches: - master - ah_var_store + - vs_971_move_bigquery_classes - name: GvsIngestTieout subclass: WDL primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/CostObservability.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/CostObservability.java index 8cfca455677..36ee0f33336 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/CostObservability.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/CostObservability.java @@ -13,7 +13,7 @@ import java.io.IOException; import java.util.Date; -import static org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; +import static org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; public class CostObservability { static final Logger logger = LogManager.getLogger(org.broadinstitute.hellbender.tools.gvs.common.CostObservability.class); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java index f9b7d95bf3b..3477400de5c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java @@ -6,8 +6,8 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader; -import org.broadinstitute.hellbender.utils.bigquery.TableReference; +import org.broadinstitute.hellbender.utils.gvs.bigquery.StorageAPIAvroReader; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import java.util.HashMap; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/SampleList.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/SampleList.java index 00b00c524cb..53c0f8b981c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/SampleList.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/common/SampleList.java @@ -10,9 +10,9 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.broadinstitute.hellbender.exceptions.GATKException; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryResultAndStatistics; -import org.broadinstitute.hellbender.utils.bigquery.TableReference; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryResultAndStatistics; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; public class SampleList { static final Logger logger = LogManager.getLogger(SampleList.class); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java index dd0405c3c9f..40e0a48a1e8 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java @@ -18,8 +18,8 @@ import org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger; import org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader; -import org.broadinstitute.hellbender.utils.bigquery.TableReference; +import org.broadinstitute.hellbender.utils.gvs.bigquery.StorageAPIAvroReader; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; import org.broadinstitute.hellbender.utils.gvs.bigquery.AvroFileReader; import org.broadinstitute.hellbender.utils.gvs.localsort.AvroSortingCollectionCodec; import org.broadinstitute.hellbender.utils.gvs.localsort.SortingCollection; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java index 129a4bd8b37..b74fd86454b 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java @@ -11,7 +11,7 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.gvs.common.*; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.bigquery.TableReference; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesBQ.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesBQ.java index 8afa4a90f11..93329b1dba9 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesBQ.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesBQ.java @@ -4,7 +4,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.exceptions.GATKException; -import org.broadinstitute.hellbender.utils.bigquery.TableReference; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; import org.broadinstitute.hellbender.utils.io.Resource; public class ExtractFeaturesBQ { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesEngine.java index 31939d77604..82c078cea15 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesEngine.java @@ -25,7 +25,10 @@ import org.broadinstitute.hellbender.utils.GenotypeCounts; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.bigquery.*; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.GATKAvroReader; +import org.broadinstitute.hellbender.utils.gvs.bigquery.StorageAPIAvroReaderAndBigQueryStatistics; +import org.broadinstitute.hellbender.utils.gvs.bigquery.TableReference; import org.broadinstitute.hellbender.utils.gvs.localsort.AvroSortingCollection; import org.broadinstitute.hellbender.utils.gvs.localsort.SortingCollection; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java index 989fa075464..ecbd9f119f8 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java @@ -22,7 +22,7 @@ import org.broadinstitute.hellbender.utils.GenomeLocParser; import org.broadinstitute.hellbender.utils.GenomeLocSortedSet; import org.broadinstitute.hellbender.utils.IntervalUtils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; import java.io.File; import java.io.IOException; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/LoadStatus.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/LoadStatus.java index 21e0e9e4e3b..503511c4313 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/LoadStatus.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/LoadStatus.java @@ -9,14 +9,14 @@ import org.apache.logging.log4j.Logger; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryResultAndStatistics; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryResultAndStatistics; import org.json.JSONArray; import org.json.JSONObject; import java.io.IOException; -import static org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; +import static org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; public class LoadStatus { static final Logger logger = LogManager.getLogger(org.broadinstitute.hellbender.tools.gvs.ingest.LoadStatus.class); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/RefCreator.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/RefCreator.java index a442999e07b..1a347736b9a 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/RefCreator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/RefCreator.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.utils.GenomeLocParser; import org.broadinstitute.hellbender.utils.GenomeLocSortedSet; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; import java.io.File; import java.io.IOException; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VcfHeaderLineScratchCreator.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VcfHeaderLineScratchCreator.java index a355665039f..8ef91f9c8c5 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VcfHeaderLineScratchCreator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VcfHeaderLineScratchCreator.java @@ -3,12 +3,11 @@ import com.google.protobuf.Descriptors; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; import org.broadinstitute.hellbender.utils.gvs.bigquery.PendingBQWriter; import org.json.JSONObject; import java.io.IOException; -import java.util.List; import java.util.Map; import java.util.concurrent.ExecutionException; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VetCreator.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VetCreator.java index 1f4a5415702..aec23295f7d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VetCreator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VetCreator.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.tools.gvs.common.CommonCode; import org.broadinstitute.hellbender.tools.gvs.common.IngestConstants; import org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; +import org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils; import org.broadinstitute.hellbender.utils.gvs.bigquery.PendingBQWriter; import org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter; import org.json.JSONObject; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/AvroFileReader.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/AvroFileReader.java index b15449e0d73..93c9863a551 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/AvroFileReader.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/AvroFileReader.java @@ -7,7 +7,6 @@ import org.apache.avro.io.DatumReader; import org.broadinstitute.hellbender.engine.GATKPath; import org.broadinstitute.hellbender.exceptions.GATKException; -import org.broadinstitute.hellbender.utils.bigquery.GATKAvroReader; import java.io.IOException; import java.util.Iterator; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryResultAndStatistics.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryResultAndStatistics.java similarity index 88% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryResultAndStatistics.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryResultAndStatistics.java index bb49d82011c..cc878e54b5a 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryResultAndStatistics.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryResultAndStatistics.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.cloud.bigquery.JobStatistics; import com.google.cloud.bigquery.TableResult; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java index e4c2f1fbde3..959923f401c 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.cloud.bigquery.*; import io.grpc.StatusRuntimeException; @@ -415,12 +415,12 @@ private static long getQueryCostBytesProcessedEstimate(String queryString, Strin return bytesProcessed; } public static StorageAPIAvroReaderAndBigQueryStatistics executeQueryWithStorageAPI(final String queryString, - final List fieldsToRetrieve, - final String projectID, - final String datasetID, - final String userDefinedFunctions, - final boolean runQueryInBatchMode, - Map labels) { + final List fieldsToRetrieve, + final String projectID, + final String datasetID, + final String userDefinedFunctions, + final boolean runQueryInBatchMode, + Map labels) { final String tempTableName = String.format("%s_%s", "temp_table", UUID.randomUUID().toString().replace('-', '_')); final String tempTableFullyQualified = String.format("%s.%s.%s", projectID, datasetID, tempTableName); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/CommittedBQWriter.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/CommittedBQWriter.java index 98ac7053699..fed674c6213 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/CommittedBQWriter.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/CommittedBQWriter.java @@ -15,7 +15,7 @@ import java.io.IOException; import java.util.concurrent.ExecutionException; -import static org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; +import static org.broadinstitute.hellbender.utils.gvs.bigquery.BigQueryUtils.extractCausalStatusRuntimeExceptionOrThrow; public class CommittedBQWriter implements AutoCloseable { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/GATKAvroReader.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/GATKAvroReader.java similarity index 79% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/GATKAvroReader.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/GATKAvroReader.java index 9080e12c48b..85e256d74b6 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/GATKAvroReader.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/GATKAvroReader.java @@ -1,8 +1,8 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import htsjdk.samtools.util.CloseableIterator; import org.apache.avro.generic.GenericRecord; public interface GATKAvroReader extends Iterable, CloseableIterator { org.apache.avro.Schema getSchema(); -} \ No newline at end of file +} diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReader.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReader.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReader.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReader.java index add9b42fd95..f140e7dd7f7 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReader.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReader.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.cloud.bigquery.storage.v1.AvroRows; import com.google.cloud.bigquery.storage.v1.BigQueryReadClient; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java similarity index 89% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java index 68871a504b4..8499593f39a 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/StorageAPIAvroReaderAndBigQueryStatistics.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.cloud.bigquery.JobStatistics; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/TableReference.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/TableReference.java similarity index 96% rename from src/main/java/org/broadinstitute/hellbender/utils/bigquery/TableReference.java rename to src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/TableReference.java index 49db6c22e2d..66898d7cb32 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/TableReference.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/TableReference.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.common.collect.ImmutableList; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtilsUnitTest.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtilsUnitTest.java rename to src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtilsUnitTest.java index e616deda82b..6af2394e72d 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtilsUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.bigquery; +package org.broadinstitute.hellbender.utils.gvs.bigquery; import com.google.cloud.bigquery.FieldValueList; import org.apache.avro.generic.GenericRecord; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/LoadStatusBQTest.java b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/LoadStatusBQTest.java index 26bbf922c0b..c4bb81b233e 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/LoadStatusBQTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/LoadStatusBQTest.java @@ -3,7 +3,6 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils; import org.broadinstitute.hellbender.tools.gvs.ingest.LoadStatus; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; import org.testng.Assert; import org.testng.annotations.AfterTest; import org.testng.annotations.BeforeTest; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/PendingBQWriterTest.java b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/PendingBQWriterTest.java index 69006a74e16..930f4d5bca6 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/PendingBQWriterTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/gvs/bigquery/PendingBQWriterTest.java @@ -3,8 +3,6 @@ import com.google.cloud.bigquery.FieldValueList; import com.google.protobuf.Descriptors; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryResultAndStatistics; -import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; import org.json.JSONObject; import org.testng.Assert; import org.testng.annotations.AfterTest;