{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/203503668","pull_request_review_id":138407054,"id":203503668,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwMzUwMzY2OA==","diff_hunk":"@@ -50,34 +50,34 @@ GATKRead apply(final ClippingRepresentation algorithm, final GATKRead originalRe\n             //   because you're not guaranteed to get a pointer to the actual array of bytes in the GATKRead\n             case WRITE_NS: {\n                 final GATKRead readCopied = originalRead.copy();\n-                applyWRITE_NS(readCopied);\n+                applyWriteNs(readCopied);\n                 return readCopied;\n             }\n \n             case WRITE_Q0S: {\n                 final GATKRead readCopied = originalRead.copy();\n-                applyWRITE_Q0S(readCopied);\n+                applyWriteQ0s(readCopied);\n                 return readCopied;\n             }\n \n             case WRITE_NS_Q0S: {\n                 final GATKRead readCopied = originalRead.copy();\n-                applyWRITE_NS(readCopied);\n-                applyWRITE_Q0S(readCopied);\n+                applyWriteNs(readCopied);\n+                applyWriteQ0s(readCopied);\n                 return readCopied;\n             }\n \n             case HARDCLIP_BASES: {\n                 //Note: passing the original read here because the read is copied right away inside the method\n-                return applyHARDCLIP_BASES(originalRead, start, stop);\n+                return applyHardclipBases(originalRead, start, stop);\n             }\n \n             case SOFTCLIP_BASES: {\n-                return applySOFTCLIP_BASES(originalRead.copy(), runAsserts);\n+                return applySoftClipBases(originalRead.copy(), runAsserts);","path":"src/main/java/org/broadinstitute/hellbender/utils/clipping/ClippingOp.java","position":33,"original_position":33,"commit_id":"3d143e8128699539ac33a47da404f2b5280ac9da","original_commit_id":"3d143e8128699539ac33a47da404f2b5280ac9da","user":{"login":"TedBrookings","id":6463752,"node_id":"MDQ6VXNlcjY0NjM3NTI=","avatar_url":"https://avatars2.githubusercontent.com/u/6463752?v=4","gravatar_id":"","url":"https://api.github.com/users/TedBrookings","html_url":"https://github.com/TedBrookings","followers_url":"https://api.github.com/users/TedBrookings/followers","following_url":"https://api.github.com/users/TedBrookings/following{/other_user}","gists_url":"https://api.github.com/users/TedBrookings/gists{/gist_id}","starred_url":"https://api.github.com/users/TedBrookings/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TedBrookings/subscriptions","organizations_url":"https://api.github.com/users/TedBrookings/orgs","repos_url":"https://api.github.com/users/TedBrookings/repos","events_url":"https://api.github.com/users/TedBrookings/events{/privacy}","received_events_url":"https://api.github.com/users/TedBrookings/received_events","type":"User","site_admin":false},"body":"It seems like this should be applySoftclipBases (lower-c) based on the location of underscores and the spelling of applyHardclipBases. In either case, the \"c\" should be the same case in those two functions.","created_at":"2018-07-18T19:37:24Z","updated_at":"2018-07-18T19:37:24Z","html_url":"https://github.com/broadinstitute/gatk/pull/5030#discussion_r203503668","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/5030","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/203503668"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/5030#discussion_r203503668"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/5030"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/5030","id":202338741,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAyMzM4NzQx","html_url":"https://github.com/broadinstitute/gatk/pull/5030","diff_url":"https://github.com/broadinstitute/gatk/pull/5030.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/5030.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5030","number":5030,"state":"open","locked":false,"title":"Camel-cased some methods in 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