{"action":"created","issue":{"url":"https://api.github.com/repos/magicDGS/ReadTools/issues/238","repository_url":"https://api.github.com/repos/magicDGS/ReadTools","labels_url":"https://api.github.com/repos/magicDGS/ReadTools/issues/238/labels{/name}","comments_url":"https://api.github.com/repos/magicDGS/ReadTools/issues/238/comments","events_url":"https://api.github.com/repos/magicDGS/ReadTools/issues/238/events","html_url":"https://github.com/magicDGS/ReadTools/pull/238","id":230682500,"number":238,"title":"Implement Barclay documentation 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#182\r\n\r\n* Add basic Barclay documentation framework\r\n* Jekyll templates\r\n* Annotate documented features\r\n* Make public argument collection to allow their use in the doc generation"},"comment":{"url":"https://api.github.com/repos/magicDGS/ReadTools/issues/comments/305748474","html_url":"https://github.com/magicDGS/ReadTools/pull/238#issuecomment-305748474","issue_url":"https://api.github.com/repos/magicDGS/ReadTools/issues/238","id":305748474,"user":{"login":"codecov[bot]","id":22429695,"avatar_url":"https://avatars1.githubusercontent.com/in/254?v=3","gravatar_id":"","url":"https://api.github.com/users/codecov%5Bbot%5D","html_url":"https://github.com/apps/codecov","followers_url":"https://api.github.com/users/codecov%5Bbot%5D/followers","following_url":"https://api.github.com/users/codecov%5Bbot%5D/following{/other_user}","gists_url":"https://api.github.com/users/codecov%5Bbot%5D/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov%5Bbot%5D/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov%5Bbot%5D/subscriptions","organizations_url":"https://api.github.com/users/codecov%5Bbot%5D/orgs","repos_url":"https://api.github.com/users/codecov%5Bbot%5D/repos","events_url":"https://api.github.com/users/codecov%5Bbot%5D/events{/privacy}","received_events_url":"https://api.github.com/users/codecov%5Bbot%5D/received_events","type":"Bot","site_admin":false},"created_at":"2017-06-02T10:18:45Z","updated_at":"2017-06-02T10:18:45Z","body":"# [Codecov](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=h1) Report\n> Merging [#238](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=desc) into [master](https://codecov.io/gh/magicDGS/ReadTools/commit/dbbce471651b6662feb2e61c241e052e3b8b71a5?src=pr&el=desc) will **increase** coverage by `0.045%`.\n> The diff coverage is `95.349%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/magicDGS/ReadTools/pull/238/graphs/tree.svg?width=650&height=150&src=pr&token=ijrOk8gNhi)](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree)\n\n```diff\n@@               Coverage Diff               @@\n##              master      #238       +/-   ##\n===============================================\n+ Coverage     91.744%   91.789%   +0.045%     \n- Complexity       755       772       +17     \n===============================================\n  Files             76        79        +3     \n  Lines           2144      2180       +36     \n  Branches         240       243        +3     \n===============================================\n+ Hits            1967      2001       +34     \n- Misses           135       136        +1     \n- Partials          42        43        +1\n```\n\n\n| [Impacted Files](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree) | Coverage Δ | Complexity Δ | |\n|---|---|---|---|\n| [...s/readtools/tools/conversion/StandardizeReads.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL2NvbnZlcnNpb24vU3RhbmRhcmRpemVSZWFkcy5qYXZh) | `100% <ø> (ø)` | `6 <0> (ø)` | :arrow_down: |\n| [...ections/RTAbstractOutputBamArgumentCollection.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL2NtZC9hcmd1bWVudGNvbGxlY3Rpb25zL1JUQWJzdHJhY3RPdXRwdXRCYW1Bcmd1bWVudENvbGxlY3Rpb24uamF2YQ==) | `100% <ø> (ø)` | `7 <0> (ø)` | :arrow_down: |\n| [...adtools/tools/quality/QualityEncodingDetector.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL3F1YWxpdHkvUXVhbGl0eUVuY29kaW5nRGV0ZWN0b3IuamF2YQ==) | `69.231% <ø> (ø)` | `4 <0> (ø)` | :arrow_down: |\n| [...gicdgs/readtools/tools/distmap/ReadsToDistmap.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL2Rpc3RtYXAvUmVhZHNUb0Rpc3RtYXAuamF2YQ==) | `89.474% <ø> (ø)` | `4 <0> (ø)` | :arrow_down: |\n| [...g/magicdgs/readtools/tools/trimming/TrimReads.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL3RyaW1taW5nL1RyaW1SZWFkcy5qYXZh) | `97.015% <ø> (ø)` | `16 <0> (ø)` | :arrow_down: |\n| [...icdgs/readtools/tools/conversion/ReadsToFastq.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL2NvbnZlcnNpb24vUmVhZHNUb0Zhc3RxLmphdmE=) | `96% <ø> (ø)` | `6 <0> (ø)` | :arrow_down: |\n| [...readtools/tools/distmap/DownloadDistmapResult.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL2Rpc3RtYXAvRG93bmxvYWREaXN0bWFwUmVzdWx0LmphdmE=) | `93.333% <ø> (ø)` | `10 <0> (ø)` | :arrow_down: |\n| [...tools/tools/barcodes/AssignReadGroupByBarcode.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3Rvb2xzL2JhcmNvZGVzL0Fzc2lnblJlYWRHcm91cEJ5QmFyY29kZS5qYXZh) | `89.655% <ø> (ø)` | `8 <0> (ø)` | :arrow_down: |\n| [...tils/read/transformer/trimming/CutReadTrimmer.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3V0aWxzL3JlYWQvdHJhbnNmb3JtZXIvdHJpbW1pbmcvQ3V0UmVhZFRyaW1tZXIuamF2YQ==) | `100% <ø> (ø)` | `18 <0> (ø)` | :arrow_down: |\n| [...ls/read/transformer/trimming/TrailingNtrimmer.java](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvbWFnaWNkZ3MvcmVhZHRvb2xzL3V0aWxzL3JlYWQvdHJhbnNmb3JtZXIvdHJpbW1pbmcvVHJhaWxpbmdOdHJpbW1lci5qYXZh) | `100% <ø> (ø)` | `2 <0> (ø)` | :arrow_down: |\n| ... and [14 more](https://codecov.io/gh/magicDGS/ReadTools/pull/238?src=pr&el=tree-more) | |\n"}}
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