diff --git a/pom.xml b/pom.xml index 7f13580..12deeac 100644 --- a/pom.xml +++ b/pom.xml @@ -65,10 +65,22 @@ + + + io.netty + netty-codec-http2 + 4.1.0.Final + io.grpc grpc-all ${io.grpc.version} + + + io.netty + netty-codec-http2 + + com.google.cloud.dataflow diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java index 6e92e15..5bc96cd 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentityByState.java @@ -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 getCallSimilarityCalculatorFactory(); @@ -113,13 +110,13 @@ public static void main(String[] args) throws Exception { Pipeline p = Pipeline.create(options); PCollection processedVariants = null; - if(null != options.getSitesFilepath()) { + if (null != options.getSitesFilepath()) { // Compute IBS on a list of sites (e.g., SNPs). PCollection 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 { @@ -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.