diff --git a/build.gradle b/build.gradle
index 57004bb0bb9..c47ab45beac 100644
--- a/build.gradle
+++ b/build.gradle
@@ -65,7 +65,7 @@ final sparkVersion = System.getProperty('spark.version', '2.2.0')
final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
final disqVersion = System.getProperty('disq.version','0.1.0')
final tensorflowVersion = System.getProperty('tensorflow.version','1.9.0')
-final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.2-proto-3.0.0-beta-1+90dad1af8ce0e4d')
+final genomicsdbVersion = System.getProperty('genomicsdb.version','1.0.0.beta1')
final testNGVersion = '6.11'
// Using the shaded version to avoid conflicts between its protobuf dependency
// and that of Hadoop/Spark (either the one we reference explicitly, or the one
@@ -226,7 +226,7 @@ dependencies {
compile 'com.github.broadinstitute:picard:' + picardVersion
externalSourceConfiguration 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
- compile ('com.intel:genomicsdb:' + genomicsdbVersion) {
+ compile ('org.genomicsdb:genomicsdb:' + genomicsdbVersion) {
exclude module: 'log4j'
exclude module: 'spark-core_2.10'
exclude module: 'htsjdk'
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
index b32519e978e..377c33f8b74 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
@@ -1,7 +1,5 @@
package org.broadinstitute.hellbender.engine;
-import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
-import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.util.IOUtil;
import htsjdk.tribble.*;
@@ -20,6 +18,8 @@
import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher;
+import org.genomicsdb.model.GenomicsDBExportConfiguration;
+import org.genomicsdb.reader.GenomicsDBFeatureReader;
import java.io.File;
import java.io.IOException;
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
index 2b5736a3258..5c7ae150f88 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
@@ -1,15 +1,6 @@
package org.broadinstitute.hellbender.tools.genomicsdb;
import com.google.common.util.concurrent.ThreadFactoryBuilder;
-import com.intel.genomicsdb.GenomicsDBUtils;
-import com.intel.genomicsdb.importer.GenomicsDBImporter;
-import com.intel.genomicsdb.importer.model.ChromosomeInterval;
-import com.intel.genomicsdb.model.Coordinates;
-import com.intel.genomicsdb.model.GenomicsDBCallsetsMapProto;
-import com.intel.genomicsdb.model.GenomicsDBImportConfiguration;
-import com.intel.genomicsdb.GenomicsDBUtils;
-import com.intel.genomicsdb.model.ImportConfig;
-import com.intel.genomicsdb.model.BatchCompletionCallbackFunctionArgument;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.util.Locatable;
import htsjdk.tribble.AbstractFeatureReader;
@@ -39,6 +30,14 @@
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher;
import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
+import org.genomicsdb.GenomicsDBUtils;
+import org.genomicsdb.importer.GenomicsDBImporter;
+import org.genomicsdb.model.Coordinates;
+import org.genomicsdb.model.GenomicsDBCallsetsMapProto;
+import org.genomicsdb.model.GenomicsDBImportConfiguration;
+import org.genomicsdb.GenomicsDBUtils;
+import org.genomicsdb.model.ImportConfig;
+import org.genomicsdb.model.BatchCompletionCallbackFunctionArgument;
import java.io.IOException;
import java.nio.channels.SeekableByteChannel;
@@ -129,7 +128,7 @@
*
*
*
Developer Note
- * To read data from GenomicsDB, use the query interface {@link com.intel.genomicsdb.reader.GenomicsDBFeatureReader}
+ * To read data from GenomicsDB, use the query interface {@link org.genomicsdb.reader.GenomicsDBFeatureReader}
*/
@DocumentedFeature
@CommandLineProgramProperties(
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
index c6e91077207..04849a43b57 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
@@ -1,12 +1,12 @@
package org.broadinstitute.hellbender.tools.genomicsdb;
import com.googlecode.protobuf.format.JsonFormat;
-import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
-import com.intel.genomicsdb.model.GenomicsDBVidMapProto;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
+import org.genomicsdb.model.GenomicsDBExportConfiguration;
+import org.genomicsdb.model.GenomicsDBVidMapProto;
import java.io.File;
import java.io.IOException;
diff --git a/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java
index 0d370f8e438..ee86732dc80 100644
--- a/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java
@@ -1,6 +1,5 @@
package org.broadinstitute.hellbender.engine;
-import com.intel.genomicsdb.GenomicsDBLibLoader;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants;
@@ -9,6 +8,7 @@
import org.broadinstitute.hellbender.GATKBaseTest;
import org.broadinstitute.hellbender.testutils.GenomicsDBTestUtils;
import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
+import org.genomicsdb.GenomicsDBLibLoader;
import org.testng.Assert;
import org.testng.annotations.Test;
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
index 6effaaadb73..c842d4632f6 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
@@ -1,9 +1,5 @@
package org.broadinstitute.hellbender.tools.genomicsdb;
-import com.intel.genomicsdb.GenomicsDBUtils;
-import com.intel.genomicsdb.model.GenomicsDBExportConfiguration;
-import com.intel.genomicsdb.model.GenomicsDBVidMapProto;
-import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.tribble.AbstractFeatureReader;
@@ -30,6 +26,10 @@
import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
+import org.genomicsdb.GenomicsDBUtils;
+import org.genomicsdb.model.GenomicsDBExportConfiguration;
+import org.genomicsdb.model.GenomicsDBVidMapProto;
+import org.genomicsdb.reader.GenomicsDBFeatureReader;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportUnitTest.java
index 8f8bf7a83f3..6690ac1afa2 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportUnitTest.java
@@ -1,11 +1,11 @@
package org.broadinstitute.hellbender.tools.genomicsdb;
-import com.intel.genomicsdb.importer.GenomicsDBImporter;
import htsjdk.tribble.FeatureReader;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.GATKBaseTest;
+import org.genomicsdb.importer.GenomicsDBImporter;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;