{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/303","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/303/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/303/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/303/events","html_url":"https://github.com/samtools/bcftools/issues/303","id":100128110,"number":303,"title":"bcftools norm error?","user":{"login":"mikecho95","id":144285,"avatar_url":"https://avatars.githubusercontent.com/u/144285?v=3","gravatar_id":"","url":"https://api.github.com/users/mikecho95","html_url":"https://github.com/mikecho95","followers_url":"https://api.github.com/users/mikecho95/followers","following_url":"https://api.github.com/users/mikecho95/following{/other_user}","gists_url":"https://api.github.com/users/mikecho95/gists{/gist_id}","starred_url":"https://api.github.com/users/mikecho95/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikecho95/subscriptions","organizations_url":"https://api.github.com/users/mikecho95/orgs","repos_url":"https://api.github.com/users/mikecho95/repos","events_url":"https://api.github.com/users/mikecho95/events{/privacy}","received_events_url":"https://api.github.com/users/mikecho95/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/samtools/bcftools/labels/need-feedback","name":"need-feedback","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-08-10T17:49:51Z","updated_at":"2015-08-28T08:24:10Z","closed_at":null,"body":"Trying to clean up a file with lots of multiallelics with no support for an allele, e.g:\r\nREF A  ALT T,C  where all genotypes are 0/2.\r\nThought norm should handle this but it exits with this error: \r\nbcftools norm myFile.bcf -m - \r\n\r\nbcftools: vcfnorm.c:739: split_info_string: Assertion `ret>0' failed.\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/bcftools/issues/comments/135671365","html_url":"https://github.com/samtools/bcftools/issues/303#issuecomment-135671365","issue_url":"https://api.github.com/repos/samtools/bcftools/issues/303","id":135671365,"user":{"login":"mcshane","id":524282,"avatar_url":"https://avatars.githubusercontent.com/u/524282?v=3","gravatar_id":"","url":"https://api.github.com/users/mcshane","html_url":"https://github.com/mcshane","followers_url":"https://api.github.com/users/mcshane/followers","following_url":"https://api.github.com/users/mcshane/following{/other_user}","gists_url":"https://api.github.com/users/mcshane/gists{/gist_id}","starred_url":"https://api.github.com/users/mcshane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcshane/subscriptions","organizations_url":"https://api.github.com/users/mcshane/orgs","repos_url":"https://api.github.com/users/mcshane/repos","events_url":"https://api.github.com/users/mcshane/events{/privacy}","received_events_url":"https://api.github.com/users/mcshane/received_events","type":"User","site_admin":false},"created_at":"2015-08-28T08:24:10Z","updated_at":"2015-08-28T08:24:10Z","body":"Your INFO/ReqIncl tag is not correct in the header based on how you are using it the the body of the VCF. Instead of `Number=.,Type=String` it should be `Number=0,Type=Flag`.\r\n```\r\n##INFO=<ID=ReqIncl,Number=0,Type=Flag,Description=\"Site was required to be included in the VCF\">\r\n```\r\nWhy ReqIncl was parsed without error should be raised as a separate issue in htslib. And/or hts-specs as to whether `Number=.` should explicitly exclude 0 length values and then `bcf_get_info_values` should probably return -1 for a clash between types defined in the header and encountered in the VCF record and the vcfnorm assert should be changed to an error to indicate this error."}}