{"action":"created","issue":{"url":"https://api.github.com/repos/jts/sga/issues/104","labels_url":"https://api.github.com/repos/jts/sga/issues/104/labels{/name}","comments_url":"https://api.github.com/repos/jts/sga/issues/104/comments","events_url":"https://api.github.com/repos/jts/sga/issues/104/events","html_url":"https://github.com/jts/sga/pull/104","id":126279027,"number":104,"title":"Filter by variant type","user":{"login":"ljdursi","id":1783579,"avatar_url":"https://avatars.githubusercontent.com/u/1783579?v=3","gravatar_id":"","url":"https://api.github.com/users/ljdursi","html_url":"https://github.com/ljdursi","followers_url":"https://api.github.com/users/ljdursi/followers","following_url":"https://api.github.com/users/ljdursi/following{/other_user}","gists_url":"https://api.github.com/users/ljdursi/gists{/gist_id}","starred_url":"https://api.github.com/users/ljdursi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ljdursi/subscriptions","organizations_url":"https://api.github.com/users/ljdursi/orgs","repos_url":"https://api.github.com/users/ljdursi/repos","events_url":"https://api.github.com/users/ljdursi/events{/privacy}","received_events_url":"https://api.github.com/users/ljdursi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-12T21:23:34Z","updated_at":"2016-01-19T16:50:27Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/jts/sga/pulls/104","html_url":"https://github.com/jts/sga/pull/104","diff_url":"https://github.com/jts/sga/pull/104.diff","patch_url":"https://github.com/jts/sga/pull/104.patch"},"body":"These commits:\r\n\r\n * Add a new VCFClassification, VCF_STRUCTURAL\r\n * Add a new option to somatic-variant-filters, `--variant-type=STR`, which can be ALL/SNV/INDEL/SV, with default ALL\r\n * Have somatic-variant-filters simply pass the VCF record to stdout if the variant type of the record is not that passed in --variant-type, otherwise performs the filtering/annotating as before.\r\n\r\nI'm not sure if this is the best way to handle the command line options or not."},"comment":{"url":"https://api.github.com/repos/jts/sga/issues/comments/172914723","html_url":"https://github.com/jts/sga/pull/104#issuecomment-172914723","issue_url":"https://api.github.com/repos/jts/sga/issues/104","id":172914723,"user":{"login":"ljdursi","id":1783579,"avatar_url":"https://avatars.githubusercontent.com/u/1783579?v=3","gravatar_id":"","url":"https://api.github.com/users/ljdursi","html_url":"https://github.com/ljdursi","followers_url":"https://api.github.com/users/ljdursi/followers","following_url":"https://api.github.com/users/ljdursi/following{/other_user}","gists_url":"https://api.github.com/users/ljdursi/gists{/gist_id}","starred_url":"https://api.github.com/users/ljdursi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ljdursi/subscriptions","organizations_url":"https://api.github.com/users/ljdursi/orgs","repos_url":"https://api.github.com/users/ljdursi/repos","events_url":"https://api.github.com/users/ljdursi/events{/privacy}","received_events_url":"https://api.github.com/users/ljdursi/received_events","type":"User","site_admin":false},"created_at":"2016-01-19T16:50:27Z","updated_at":"2016-01-19T16:50:27Z","body":"Better?  Will bcftools norm decompose a complex substitution into a deletion + insertion?  I don't want the annotation pipeline to miss any \"indel\" calls even if they're COMPLEX by this definition."}}