{"action":"created","issue":{"url":"https://api.github.com/repos/moonso/vcf_parser/issues/5","labels_url":"https://api.github.com/repos/moonso/vcf_parser/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/moonso/vcf_parser/issues/5/comments","events_url":"https://api.github.com/repos/moonso/vcf_parser/issues/5/events","html_url":"https://github.com/moonso/vcf_parser/pull/5","id":57464556,"number":5,"title":"updated/fixed test_vcf.vcf and bug report","user":{"login":"dakl","id":17823,"avatar_url":"https://avatars.githubusercontent.com/u/17823?v=3","gravatar_id":"","url":"https://api.github.com/users/dakl","html_url":"https://github.com/dakl","followers_url":"https://api.github.com/users/dakl/followers","following_url":"https://api.github.com/users/dakl/following{/other_user}","gists_url":"https://api.github.com/users/dakl/gists{/gist_id}","starred_url":"https://api.github.com/users/dakl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dakl/subscriptions","organizations_url":"https://api.github.com/users/dakl/orgs","repos_url":"https://api.github.com/users/dakl/repos","events_url":"https://api.github.com/users/dakl/events{/privacy}","received_events_url":"https://api.github.com/users/dakl/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-02-12T14:10:49Z","updated_at":"2015-02-12T15:35:08Z","closed_at":"2015-02-12T15:23:55Z","pull_request":{"url":"https://api.github.com/repos/moonso/vcf_parser/pulls/5","html_url":"https://github.com/moonso/vcf_parser/pull/5","diff_url":"https://github.com/moonso/vcf_parser/pull/5.diff","patch_url":"https://github.com/moonso/vcf_parser/pull/5.patch"},"body":"Hi Måns, \r\n\r\nI updated test_vcf.vcf in the following ways:\r\n\r\n1. Fix missing newline for ##contig\r\n2. Add explicit FORMAT tags for GT,GQ,AD and DP tags\r\n3. Set DP_HIST to correct value(s). Number=R means one value per allele incl REF. \r\n4. Set fileformat to 4.2 (Number=R is a VCFv4.2 feature)\r\n5. Removed TP from FORMAT which has no value fro mother or proband, and no corresponding `##FORMAT` in the header\r\n\r\nThis revealed a bug: The --split option does not split DP_HIST correctly (or at all it seems like): \r\n\r\n```\r\n3\t947379\t.\tA\tT\t100\tPASS\tMQ=1;CNT=5;DP_HIST=12,43,22\tGT:GQ:AD:DP\t1/1:60:0,7:12\t0/0:60:7,0:17\t0/1:60:0,7:16\r\n3\t947379\t.\tA\tC\t100\tPASS\tMQ=1;CNT=8;DP_HIST=12,43,22\tGT:GQ:AD:DP\t0/0:60:0,0:12\t0/1:60:7,10:17\t0/1:60:0,8:16\r\n```\r\n\r\nBeing Number=R, it should have one value for each allele including ref (i.e. 3 values prior to split and 2 for biallelic variants). The code that splits INFO fields needs to check if they are `A`, `R` or `.`. \r\n\r\nCheers =)"},"comment":{"url":"https://api.github.com/repos/moonso/vcf_parser/issues/comments/74090746","html_url":"https://github.com/moonso/vcf_parser/pull/5#issuecomment-74090746","issue_url":"https://api.github.com/repos/moonso/vcf_parser/issues/5","id":74090746,"user":{"login":"dakl","id":17823,"avatar_url":"https://avatars.githubusercontent.com/u/17823?v=3","gravatar_id":"","url":"https://api.github.com/users/dakl","html_url":"https://github.com/dakl","followers_url":"https://api.github.com/users/dakl/followers","following_url":"https://api.github.com/users/dakl/following{/other_user}","gists_url":"https://api.github.com/users/dakl/gists{/gist_id}","starred_url":"https://api.github.com/users/dakl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dakl/subscriptions","organizations_url":"https://api.github.com/users/dakl/orgs","repos_url":"https://api.github.com/users/dakl/repos","events_url":"https://api.github.com/users/dakl/events{/privacy}","received_events_url":"https://api.github.com/users/dakl/received_events","type":"User","site_admin":false},"created_at":"2015-02-12T15:35:08Z","updated_at":"2015-02-12T15:35:08Z","body":"Thanks, will check it out tomorrow. I think the best behaviour for the\nfields of type `.` is to pass them along as they are to each item in split\nvariants. I guess the alternative would be to drop them completely, which I\ndon't think makes sense.\n\ncheers\nDaniel\n\nOn Thu, Feb 12, 2015 at 4:24 PM, Måns Magnusson <notifications@github.com>\nwrote:\n\n> It should split R-field proper noe.\n> Thank you for this one!\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/moonso/vcf_parser/pull/5#issuecomment-74088782>.\n>\n"}}