diff --git a/pom.xml b/pom.xml
index cca3f0a..3b22adb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -141,7 +141,7 @@
com.google.guava
guava
- 18.0
+ 19.0
gov.nist.math.jama
@@ -343,6 +343,13 @@
org.apache.maven.plugins
maven-jar-plugin
2.6
+
+
+
+ test-jar
+
+
+
diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java
index 73bb0b2..c41ab76 100644
--- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java
+++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java
@@ -19,7 +19,6 @@
import com.google.cloud.dataflow.sdk.options.Description;
import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory;
import com.google.cloud.dataflow.sdk.options.Validation.Required;
-import com.google.cloud.dataflow.sdk.repackaged.com.google.common.collect.ImmutableSet;
import com.google.cloud.dataflow.sdk.transforms.Create;
import com.google.cloud.dataflow.sdk.transforms.DoFn;
import com.google.cloud.dataflow.sdk.transforms.ParDo;
@@ -34,6 +33,7 @@
import com.google.common.base.CharMatcher;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
+import com.google.common.collect.ImmutableSet;
import com.google.common.io.Files;
import com.google.genomics.v1.StreamVariantsRequest;
import com.google.genomics.v1.Variant;
@@ -149,7 +149,7 @@ public static void main(String[] args) throws IOException, GeneralSecurityExcept
ImmutableSet
.builder()
.addAll(
- Splitter.on(CharMatcher.BREAKING_WHITESPACE).omitEmptyStrings().trimResults()
+ Splitter.on(CharMatcher.breakingWhitespace()).omitEmptyStrings().trimResults()
.split(fileContents)).build();
LOG.info("The pipeline will identify and write to Cloud Storage variants "
+ "private to " + callSetIds.size() + " genomes with callSetIds: " + callSetIds);
diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java
index bc8db4b..b9dc391 100644
--- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java
+++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java
@@ -13,7 +13,6 @@
*/
package com.google.cloud.genomics.dataflow.pipelines;
-import com.google.api.client.repackaged.com.google.common.base.Strings;
import com.google.api.services.storage.Storage;
import com.google.cloud.dataflow.sdk.Pipeline;
import com.google.cloud.dataflow.sdk.coders.Coder;
@@ -45,6 +44,7 @@
import com.google.cloud.genomics.utils.ShardUtils;
import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter;
import com.google.common.base.Preconditions;
+import com.google.common.base.Strings;
import com.google.common.collect.Lists;
import com.google.genomics.v1.Read;
import com.google.genomics.v1.StreamReadsRequest;
diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java
index b1233fa..214758c 100644
--- a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java
+++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java
@@ -13,11 +13,11 @@
*/
package com.google.cloud.genomics.dataflow.utils;
-import com.google.api.client.repackaged.com.google.common.base.Strings;
import com.google.cloud.dataflow.sdk.options.Description;
import com.google.cloud.dataflow.sdk.options.Validation;
import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath;
import com.google.common.base.Preconditions;
+import com.google.common.base.Strings;
/**
* A common options class for all pipelines that write their analysis results to GCS files.