{"action":"created","issue":{"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/47","labels_url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/47/comments","events_url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/47/events","html_url":"https://github.com/dnanexus-rnd/GLnexus/pull/47","id":117251588,"number":47,"title":"Adding sanity tests to check the validity of the gVCF data","user":{"login":"orodeh","id":7037561,"avatar_url":"https://avatars.githubusercontent.com/u/7037561?v=3","gravatar_id":"","url":"https://api.github.com/users/orodeh","html_url":"https://github.com/orodeh","followers_url":"https://api.github.com/users/orodeh/followers","following_url":"https://api.github.com/users/orodeh/following{/other_user}","gists_url":"https://api.github.com/users/orodeh/gists{/gist_id}","starred_url":"https://api.github.com/users/orodeh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orodeh/subscriptions","organizations_url":"https://api.github.com/users/orodeh/orgs","repos_url":"https://api.github.com/users/orodeh/repos","events_url":"https://api.github.com/users/orodeh/events{/privacy}","received_events_url":"https://api.github.com/users/orodeh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"mlin","id":356550,"avatar_url":"https://avatars.githubusercontent.com/u/356550?v=3","gravatar_id":"","url":"https://api.github.com/users/mlin","html_url":"https://github.com/mlin","followers_url":"https://api.github.com/users/mlin/followers","following_url":"https://api.github.com/users/mlin/following{/other_user}","gists_url":"https://api.github.com/users/mlin/gists{/gist_id}","starred_url":"https://api.github.com/users/mlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlin/subscriptions","organizations_url":"https://api.github.com/users/mlin/orgs","repos_url":"https://api.github.com/users/mlin/repos","events_url":"https://api.github.com/users/mlin/events{/privacy}","received_events_url":"https://api.github.com/users/mlin/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-11-17T00:26:52Z","updated_at":"2015-11-17T22:28:02Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/pulls/47","html_url":"https://github.com/dnanexus-rnd/GLnexus/pull/47","diff_url":"https://github.com/dnanexus-rnd/GLnexus/pull/47.diff","patch_url":"https://github.com/dnanexus-rnd/GLnexus/pull/47.patch"},"body":"This implements the following additional checks on gVCFs as we load them: \r\n1) <= 1,000 contigs (due to bucket key schema)\r\n2) contig length <= 1e10 (ditto)\r\n3) on ingestion, check gVCF records don't pass end of contig\r\n4) DNA regexp for gVCF REF and ALT alleles\r\n"},"comment":{"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/comments/157530412","html_url":"https://github.com/dnanexus-rnd/GLnexus/pull/47#issuecomment-157530412","issue_url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/issues/47","id":157530412,"user":{"login":"mlin","id":356550,"avatar_url":"https://avatars.githubusercontent.com/u/356550?v=3","gravatar_id":"","url":"https://api.github.com/users/mlin","html_url":"https://github.com/mlin","followers_url":"https://api.github.com/users/mlin/followers","following_url":"https://api.github.com/users/mlin/following{/other_user}","gists_url":"https://api.github.com/users/mlin/gists{/gist_id}","starred_url":"https://api.github.com/users/mlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlin/subscriptions","organizations_url":"https://api.github.com/users/mlin/orgs","repos_url":"https://api.github.com/users/mlin/repos","events_url":"https://api.github.com/users/mlin/events{/privacy}","received_events_url":"https://api.github.com/users/mlin/received_events","type":"User","site_admin":false},"created_at":"2015-11-17T22:28:02Z","updated_at":"2015-11-17T22:28:02Z","body":"General comment: I think the validation of the number and size of contigs would be better performed in `BCFKeyValueData::InitializeDB`. We then require that all gVCF files we ingest have the same contigs as the database was initialized with, so given that check, validating the contigs in every file is redundant. (Actually we don't check the sizes the right now, there's a TODO to this effect you could take care of)"}}