{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4964","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4964/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4964/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4964/events","html_url":"https://github.com/broadinstitute/gatk/pull/4964","id":336734305,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk4MTE3MjEz","number":4964,"title":"Added a new `Walker` abstract class to be used for all built-in 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the following methods to `GATKTool`:\r\n\r\n- `getReferenceDataSource()`\r\n- `getReadsDataSource()`\r\n- `getFeatureManager()`\r\n\r\n`Walker` inherits directly from `GATKTool` and overrides these methods to throw an exception if they are called.\r\n\r\nNo walker should need to directly access the data."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/404134765","html_url":"https://github.com/broadinstitute/gatk/pull/4964#issuecomment-404134765","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4964","id":404134765,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDEzNDc2NQ==","user":{"login":"magicDGS","id":7352559,"node_id":"MDQ6VXNlcjczNTI1NTk=","avatar_url":"https://avatars0.githubusercontent.com/u/7352559?v=4","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"created_at":"2018-07-11T11:20:30Z","updated_at":"2018-07-11T11:20:30Z","author_association":"CONTRIBUTOR","body":"I am aware that those methods should be definetively implemented in the abstract class - but it could be recommended *NOT TO OVERRIDE* unless you know what you are doing. I know the problems of having them exposed, but also I can see some potential to be accessible from an implemented walker when the user knows what is doing..."}}
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