{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/712","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/712/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/712/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/712/events","html_url":"https://github.com/broadinstitute/picard/pull/712","id":195532293,"number":712,"title":"Default output for CreateSequenceDictionary","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-12-14T13:36:09Z","updated_at":"2016-12-14T15:32:15Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/712","html_url":"https://github.com/broadinstitute/picard/pull/712","diff_url":"https://github.com/broadinstitute/picard/pull/712.diff","patch_url":"https://github.com/broadinstitute/picard/pull/712.patch"},"body":"### Description\r\n\r\n`CreateSequenceDictionary` requires always to specified the output name, but GATK programs assumes that the file name is the FASTA name without the extension and ending in __.dict__. Thus, I included the following changes:\r\n* Optional output argument with updated documentation for default behavior.\r\n* Sets the output name as in the GATK framework (port of https://github.com/broadinstitute/gatk/pull/2243) if no one is provided.\r\n* Test for default output name.\r\n\r\n----\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- [x] 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\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/267064482","html_url":"https://github.com/broadinstitute/picard/pull/712#issuecomment-267064482","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/712","id":267064482,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2016-12-14T15:32:15Z","updated_at":"2016-12-14T15:32:15Z","body":"\n[![Coverage Status](https://coveralls.io/builds/9279064/badge)](https://coveralls.io/builds/9279064)\n\nCoverage increased (+0.01%) to 71.071% when pulling **bdb4cd86f22c9c8dbbd9de7fdc7bf303e9a2c943 on magicDGS:dgs_default_output_dict** into **0cb2985ae59cd5b77221f42366d5fe9114c64c49 on broadinstitute:master**.\n"}}
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