{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/39698375","id":39698375,"diff_hunk":"@@ -0,0 +1,205 @@\n+package org.broadinstitute.hellbender.engine.spark;\n+\n+import com.google.api.services.genomics.model.Read;\n+import com.google.cloud.dataflow.sdk.values.KV;\n+import com.google.common.collect.Lists;\n+import htsjdk.samtools.SAMRecord;\n+import org.broadinstitute.hellbender.engine.dataflow.datasources.ReadContextData;\n+import org.broadinstitute.hellbender.engine.dataflow.datasources.ReferenceShard;\n+import org.broadinstitute.hellbender.engine.dataflow.datasources.VariantShard;\n+import org.broadinstitute.hellbender.exceptions.GATKException;\n+import org.broadinstitute.hellbender.utils.SimpleInterval;\n+import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils;\n+import org.broadinstitute.hellbender.utils.read.GATKRead;\n+import org.broadinstitute.hellbender.utils.reference.ReferenceBases;\n+import org.broadinstitute.hellbender.utils.test.FakeReferenceSource;\n+import org.broadinstitute.hellbender.utils.variant.SkeletonVariant;\n+import org.broadinstitute.hellbender.utils.variant.Variant;\n+import org.testng.Assert;\n+import org.testng.annotations.Test;\n+\n+import java.util.Arrays;\n+import java.util.List;\n+import java.util.UUID;\n+\n+/**\n+ * ReadsPreprocessingPipelineTestData contains coordinated test data that can be used in the many transforms that\n+ * are a part of the ReadsPreprocessingPipeline.\n+ */\n+public class ReadsPreprocessingPipelineSparkTestData {","path":"src/test/java/org/broadinstitute/hellbender/engine/spark/ReadsPreprocessingPipelineSparkTestData.java","position":29,"original_position":29,"commit_id":"deb395380f0bc99d064cda6be1086a1fd925ff4e","original_commit_id":"deb395380f0bc99d064cda6be1086a1fd925ff4e","user":{"login":"davidadamsphd","id":12084283,"avatar_url":"https://avatars.githubusercontent.com/u/12084283?v=3","gravatar_id":"","url":"https://api.github.com/users/davidadamsphd","html_url":"https://github.com/davidadamsphd","followers_url":"https://api.github.com/users/davidadamsphd/followers","following_url":"https://api.github.com/users/davidadamsphd/following{/other_user}","gists_url":"https://api.github.com/users/davidadamsphd/gists{/gist_id}","starred_url":"https://api.github.com/users/davidadamsphd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidadamsphd/subscriptions","organizations_url":"https://api.github.com/users/davidadamsphd/orgs","repos_url":"https://api.github.com/users/davidadamsphd/repos","events_url":"https://api.github.com/users/davidadamsphd/events{/privacy}","received_events_url":"https://api.github.com/users/davidadamsphd/received_events","type":"User","site_admin":false},"body":"What's changed here relative to ReadsPreprocessingPipelineTestData?","created_at":"2015-09-16T23:38:23Z","updated_at":"2015-09-16T23:38:23Z","html_url":"https://github.com/broadinstitute/hellbender/pull/899#discussion_r39698375","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/899","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/39698375"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/899#discussion_r39698375"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/899"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/899","id":45165035,"html_url":"https://github.com/broadinstitute/hellbender/pull/899","diff_url":"https://github.com/broadinstitute/hellbender/pull/899.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/899.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/899","number":899,"state":"open","locked":false,"title":"Add a Spark Kryo serializer for SAMRecords.","user":{"login":"tomwhite","id":85085,"avatar_url":"https://avatars.githubusercontent.com/u/85085?v=3","gravatar_id":"","url":"https://api.github.com/users/tomwhite","html_url":"https://github.com/tomwhite","followers_url":"https://api.github.com/users/tomwhite/followers","following_url":"https://api.github.com/users/tomwhite/following{/other_user}","gists_url":"https://api.github.com/users/tomwhite/gists{/gist_id}","starred_url":"https://api.github.com/users/tomwhite/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomwhite/subscriptions","organizations_url":"https://api.github.com/users/tomwhite/orgs","repos_url":"https://api.github.com/users/tomwhite/repos","events_url":"https://api.github.com/users/tomwhite/events{/privacy}","received_events_url":"https://api.github.com/users/tomwhite/received_events","type":"User","site_admin":false},"body":"This improves the serialized size considerably, which has a very big effect on the amount of data going through the shuffle.\r\n\r\n* SAMRecordToGATKReadAdapterSerializer uses BAMRecordCodec for a compact serialization format.\r\n* Record headers are not needed since GATKRead is intended to abstract them away. 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