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Bump io.netty dependency. #198

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Jun 6, 2016
Merged

Bump io.netty dependency. #198

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743a361
Minor cleanup.
deflaux Jun 6, 2016
839c49c
Bump io.netty dependency.
deflaux Jun 6, 2016
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12 changes: 12 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -65,10 +65,22 @@
</distributionManagement>

<dependencies>
<!-- Remove this later https://github.com/googlegenomics/dataflow-java/issues/197 -->
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-codec-http2</artifactId>
<version>4.1.0.Final</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
<version>${io.grpc.version}</version>
<exclusions>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-codec-http2</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.cloud.dataflow</groupId>
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9 changes: 3 additions & 6 deletions src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java
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Expand Up @@ -75,9 +75,6 @@ public static interface Options extends
@Default.String("10473108253681171589")
String getVariantSetId();

@Override
void setVariantSetId(String variantSetId);

@Description("The class that determines the strategy for calculating the similarity of alleles.")
@Default.Class(SharedMinorAllelesCalculatorFactory.class)
Class<? extends CallSimilarityCalculatorFactory> getCallSimilarityCalculatorFactory();
Expand Down Expand Up @@ -113,13 +110,13 @@ public static void main(String[] args) throws Exception {
Pipeline p = Pipeline.create(options);
PCollection<Variant> processedVariants = null;

if(null != options.getSitesFilepath()) {
if (null != options.getSitesFilepath()) {
// Compute IBS on a list of sites (e.g., SNPs).
PCollection<StreamVariantsRequest> requests = p.apply(TextIO.Read.named("ReadSites")
.from(options.getSitesFilepath()))
.apply(new SitesToShards.SitesToStreamVariantsShardsTransform(prototype));

if(options.getHasNonVariantSegments()) {
if (options.getHasNonVariantSegments()) {
processedVariants = requests.apply(
new JoinNonVariantSegmentsWithVariants.RetrieveAndCombineTransform(auth, VARIANT_FIELDS));
} else {
Expand All @@ -136,7 +133,7 @@ public static void main(String[] args) throws Exception {
.apply(Create.of(requests))
.apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS));

if(options.getHasNonVariantSegments()) {
if (options.getHasNonVariantSegments()) {
// Note that this is less exact compared to the above approach on sites.
// When not run on a whole chromosome or genome, any non-variant segments at the beginning of the region(s)
// are not considered due to the STRICT shard boundary used to avoid repeated data.
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