{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/817","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/817/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/817/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/817/events","html_url":"https://github.com/broadinstitute/picard/pull/817","id":229357638,"number":817,"title":"Switch to Barclay command line parser(s)","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars2.githubusercontent.com/u/10062863?v=4","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2017-05-17T13:45:20Z","updated_at":"2017-07-18T17:33:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/817","html_url":"https://github.com/broadinstitute/picard/pull/817","diff_url":"https://github.com/broadinstitute/picard/pull/817.diff","patch_url":"https://github.com/broadinstitute/picard/pull/817.patch"},"body":"### Description\r\n\r\nChanges to use the Barclay command line parser(s), as discussed [here](https://github.com/broadinstitute/picard/issues/786).\r\n\r\nThere are 5 separate commits to make this somewhat easier to review:\r\n\r\n1. Changes to Barclay package/class names, annotations, attributes, and imports only.\r\n2. Switch to the Barclay version of the existing parser. This mostly consists of removal of the existing command line parser, and changes to CommandLineProgram to use the Barclay version of the Picard parser.\r\n3. Use @ArgumentCollection, remove overridable. With this commit, the tests pass using the Barclay version of the Picard parser.\r\n4. Add ability to toggle between the two Barclay parsers. This includes property-based opt-in CLP toggling (default uses the existing parser); Gradle changes to generate a second artifact that uses the Barclay parser; minor changes to tools to get the tests to pass with both parsers, and a few changes required for tools that have no tests.\r\n5. Gradle changes for the Barclay documentation generation process. These changes are build-only, plus the addition of the @DocumentedFeature annotation (required to make a tool a doc target) to use to verify this process.\r\n\r\nThere is one tool (DownsampleSam, and three more in picard-private) that use “R” as a command line argument for something other than reference, which is problematic for the @ArgumentCollection pattern. I’ve temporarily changed these to use a different short name. If thats  not workable, its possible to keep them as is, though it will require a little bit of ugly code and a typecast.\r\n\r\n(There is also a separate branch for [picard-private](https://github.com/broadinstitute/picard-private/tree/cn_barclay) that has corresponding changes, subject to completion of this PR).\r\n\r\n### Checklist (never delete this)\r\n\r\nNever delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.\r\n\r\n#### Content\r\n- [X] Added or modified tests to cover changes and any new functionality\r\n- [ ] Edited the README / documentation (if applicable)\r\n- [X] All tests passing on Travis\r\n\r\n#### Review\r\n- [ ] Final thumbs-up from reviewer\r\n- [ ] Rebase, squash and reword as applicable\r\n\r\nFor more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/316138512","html_url":"https://github.com/broadinstitute/picard/pull/817#issuecomment-316138512","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/817","id":316138512,"user":{"login":"pshapiro4broad","id":1799360,"avatar_url":"https://avatars2.githubusercontent.com/u/1799360?v=4","gravatar_id":"","url":"https://api.github.com/users/pshapiro4broad","html_url":"https://github.com/pshapiro4broad","followers_url":"https://api.github.com/users/pshapiro4broad/followers","following_url":"https://api.github.com/users/pshapiro4broad/following{/other_user}","gists_url":"https://api.github.com/users/pshapiro4broad/gists{/gist_id}","starred_url":"https://api.github.com/users/pshapiro4broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pshapiro4broad/subscriptions","organizations_url":"https://api.github.com/users/pshapiro4broad/orgs","repos_url":"https://api.github.com/users/pshapiro4broad/repos","events_url":"https://api.github.com/users/pshapiro4broad/events{/privacy}","received_events_url":"https://api.github.com/users/pshapiro4broad/received_events","type":"User","site_admin":false},"created_at":"2017-07-18T17:33:54Z","updated_at":"2017-07-18T17:33:54Z","body":"Looks ok to me 👍 "}}
{"actor":{"display_login":"pshapiro4broad"}}