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The input file\n+     * should be the output of as RunSGAViaProcessBuilderOnSpark.\n+     */\n+    static JavaPairRDD<String, ContigsCollection> loadContigsCollectionKeyedByAssemblyId(final JavaSparkContext ctx, final String inputPath) {\n+        final JavaRDD<String> inputAssemblies = ctx.textFile(inputPath).cache();\n+\n+        final JavaPairRDD<String, String> contigCollectionByBreakpointId =\n+                inputAssemblies\n+                        .flatMapToPair(RunSGAViaProcessBuilderOnSpark::splitAssemblyLine);\n+\n+        return contigCollectionByBreakpointId.mapValues(ContigsCollection::fromPackedFasta);\n+    }\n+\n+    /**\n+     * input format is the text representation of an alignment region\n+     * @param alignedAssembedContigLine An input line with the tab-separated fields of an alignment region\n+     * @return A tuple with the breakpoint ID and string representation of an BreakpointAlignment, or an empty iterator if the line did not have two comma-separated values\n+     */\n+    static AlignmentRegion parseAlignedAssembledContigLine(final String alignedAssembedContigLine) {","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/sv/AlignAssembledContigsSpark.java","position":111,"original_position":111,"commit_id":"e20d8b679a2d1adc5743c2d42a875cef33c3f9fb","original_commit_id":"e20d8b679a2d1adc5743c2d42a875cef33c3f9fb","user":{"login":"cwhelan","id":709477,"avatar_url":"https://avatars.githubusercontent.com/u/709477?v=3","gravatar_id":"","url":"https://api.github.com/users/cwhelan","html_url":"https://github.com/cwhelan","followers_url":"https://api.github.com/users/cwhelan/followers","following_url":"https://api.github.com/users/cwhelan/following{/other_user}","gists_url":"https://api.github.com/users/cwhelan/gists{/gist_id}","starred_url":"https://api.github.com/users/cwhelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cwhelan/subscriptions","organizations_url":"https://api.github.com/users/cwhelan/orgs","repos_url":"https://api.github.com/users/cwhelan/repos","events_url":"https://api.github.com/users/cwhelan/events{/privacy}","received_events_url":"https://api.github.com/users/cwhelan/received_events","type":"User","site_admin":false},"body":"done","created_at":"2016-08-22T02:47:27Z","updated_at":"2016-08-22T02:47:27Z","html_url":"https://github.com/broadinstitute/gatk/pull/2079#discussion_r75612383","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2079","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/75612383"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/2079#discussion_r75612383"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/2079"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2079","id":80297596,"html_url":"https://github.com/broadinstitute/gatk/pull/2079","diff_url":"https://github.com/broadinstitute/gatk/pull/2079.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/2079.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2079","number":2079,"state":"open","locked":false,"title":"Deduplicate and filter breakpoints and call inversion variants","user":{"login":"cwhelan","id":709477,"avatar_url":"https://avatars.githubusercontent.com/u/709477?v=3","gravatar_id":"","url":"https://api.github.com/users/cwhelan","html_url":"https://github.com/cwhelan","followers_url":"https://api.github.com/users/cwhelan/followers","following_url":"https://api.github.com/users/cwhelan/following{/other_user}","gists_url":"https://api.github.com/users/cwhelan/gists{/gist_id}","starred_url":"https://api.github.com/users/cwhelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cwhelan/subscriptions","organizations_url":"https://api.github.com/users/cwhelan/orgs","repos_url":"https://api.github.com/users/cwhelan/repos","events_url":"https://api.github.com/users/cwhelan/events{/privacy}","received_events_url":"https://api.github.com/users/cwhelan/received_events","type":"User","site_admin":false},"body":"This PR adds:\r\n\r\n- A tool to take contig alignments from the AlignContigsAndCallBreakpointsSpark tool, deduplicate and filter those which have the same breakpoint structure, and add the proper annotations to the resulting VCF of called inversion events.\r\n \r\n- A similar tool that takes SAM records and does the same thing, looking at split/supplementary alignments.\r\n\r\nFor @SHuang-Broad to review. 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