{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/206353764","pull_request_review_id":141702287,"id":206353764,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwNjM1Mzc2NA==","diff_hunk":"@@ -272,44 +281,197 @@ public static AssemblyContigsClassifiedByAlignmentSignatures preprocess(final Sv\n      * {@link AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType#UNKNOWN}\n      * currently DO NOT generate any VCF yet.\n      */\n-    public static void dispatchJobs(final JavaSparkContext ctx,\n-                                    final AssemblyContigsClassifiedByAlignmentSignatures contigsByPossibleRawTypes,\n-                                    final SvDiscoveryInputMetaData svDiscoveryInputMetaData,\n-                                    final JavaRDD<GATKRead> assemblyRawAlignments,\n-                                    final boolean writeSAMFiles) {\n+    public static List<VariantContext> dispatchJobs(final JavaSparkContext ctx,\n+                                                    final AssemblyContigsClassifiedByAlignmentSignatures contigsByPossibleRawTypes,\n+                                                    final SvDiscoveryInputMetaData svDiscoveryInputMetaData,\n+                                                    final JavaRDD<GATKRead> assemblyRawAlignments,\n+                                                    final boolean writeSAMFiles) {\n \n         final String outputPrefixWithSampleName = svDiscoveryInputMetaData.getOutputPath();\n \n-        // TODO: 1/10/18 bring back read annotation, see ticket 4228\n+        final List<VariantContext> simpleChimeraVariants =\n+                extractSimpleVariants(contigsByPossibleRawTypes.simple, svDiscoveryInputMetaData, outputPrefixWithSampleName);\n+        contigsByPossibleRawTypes.simple.unpersist(false);","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java","position":null,"original_position":91,"commit_id":"7997d50db1573cc9d1db03479b6f1cf50270b615","original_commit_id":"ccd5f870392a807227b9c3c7d76ed03251081417","user":{"login":"SHuang-Broad","id":16310888,"node_id":"MDQ6VXNlcjE2MzEwODg4","avatar_url":"https://avatars3.githubusercontent.com/u/16310888?v=4","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false},"body":"Thanks! That's much better.","created_at":"2018-07-30T23:27:53Z","updated_at":"2018-07-30T23:32:26Z","html_url":"https://github.com/broadinstitute/gatk/pull/4996#discussion_r206353764","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4996","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/206353764"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/4996#discussion_r206353764"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/4996"}},"in_reply_to_id":206134659},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4996","id":200549084,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAwNTQ5MDg0","html_url":"https://github.com/broadinstitute/gatk/pull/4996","diff_url":"https://github.com/broadinstitute/gatk/pull/4996.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/4996.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4996","number":4996,"state":"open","locked":false,"title":"(SV) output merged single VCF for new interpretation 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