{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/46303750","id":46303750,"diff_hunk":"@@ -105,7 +106,14 @@ protected void runTool(final JavaSparkContext ctx) {\n         }\n \n         JavaRDD<GATKRead> initialReads = getReads();\n-        JavaRDD<GATKRead> markedReads = MarkDuplicatesSpark.mark(initialReads, getHeaderForReads(), duplicatesScoringStrategy, new OpticalDuplicateFinder());\n+        JavaRDD<GATKRead> markedReadsWithOD = MarkDuplicatesSpark.mark(initialReads, getHeaderForReads(), duplicatesScoringStrategy, new OpticalDuplicateFinder());\n+\n+        //The OD attribute was added to each read for optical dups.\n+        // Now we have to clear it to avoid polluting the output.\n+        final JavaRDD<GATKRead> markedReads = markedReadsWithOD.map(read -> {\n+            read.clearAttribute(MarkDuplicatesSparkUtils.OPTICAL_DUPLICATE_TOTAL_ATTRIBUTE_NAME);\n+            return read;\n+        });","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java","position":29,"original_position":29,"commit_id":"84a1594a8c2cb89d7bdf70abc9a106d35b0d4040","original_commit_id":"84a1594a8c2cb89d7bdf70abc9a106d35b0d4040","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"body":"Should we add an option to `MarkDuplicatesSpark` itself that allows the caller to prevent this attribute from getting added in the first place?","created_at":"2015-12-01T16:49:56Z","updated_at":"2015-12-01T16:49:56Z","html_url":"https://github.com/broadinstitute/gatk/pull/1197#discussion_r46303750","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1197","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/46303750"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1197#discussion_r46303750"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1197"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1197","id":51879626,"html_url":"https://github.com/broadinstitute/gatk/pull/1197","diff_url":"https://github.com/broadinstitute/gatk/pull/1197.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1197.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1197","number":1197,"state":"open","locked":false,"title":"reads pipeline 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