{"action":"created","issue":{"url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/61","repository_url":"https://api.github.com/repos/zkutalik/ssimp_software","labels_url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/61/labels{/name}","comments_url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/61/comments","events_url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/61/events","html_url":"https://github.com/zkutalik/ssimp_software/issues/61","id":326660945,"node_id":"MDU6SXNzdWUzMjY2NjA5NDU=","number":61,"title":"which_build_t:: unknown' failed.","user":{"login":"jimmyzliu","id":8708105,"node_id":"MDQ6VXNlcjg3MDgxMDU=","avatar_url":"https://avatars2.githubusercontent.com/u/8708105?v=4","gravatar_id":"","url":"https://api.github.com/users/jimmyzliu","html_url":"https://github.com/jimmyzliu","followers_url":"https://api.github.com/users/jimmyzliu/followers","following_url":"https://api.github.com/users/jimmyzliu/following{/other_user}","gists_url":"https://api.github.com/users/jimmyzliu/gists{/gist_id}","starred_url":"https://api.github.com/users/jimmyzliu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimmyzliu/subscriptions","organizations_url":"https://api.github.com/users/jimmyzliu/orgs","repos_url":"https://api.github.com/users/jimmyzliu/repos","events_url":"https://api.github.com/users/jimmyzliu/events{/privacy}","received_events_url":"https://api.github.com/users/jimmyzliu/received_events","type":"User","site_admin":false},"labels":[{"id":556104292,"node_id":"MDU6TGFiZWw1NTYxMDQyOTI=","url":"https://api.github.com/repos/zkutalik/ssimp_software/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":24,"created_at":"2018-05-25T20:52:37Z","updated_at":"2018-11-20T11:34:42Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI am trying to impute a small region on chromosome 21 using a custom reference panel of ~500 individuals. I receive the following error:\r\n\r\n```\r\n$ ssimp-linux-0.3 \\\r\n> --gwas chr21chunk.txt \\\r\n> --ref custom.21.vcf.gz \\\r\n> --out test.txt\r\n\r\nfile_name:chr21chunk.txt\r\n... loading the 1.7GB database of positions under three builds. This will take about a minute.  Loaded.\r\nEstimating which build (hg18/hg19/hg37) of the reference panel and the GWAS file, in caseit is necessary to modify the GWAS file to match the reference panel\r\nsome_records_from_each_chromosome.size():0\r\ncount_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based:    0 , 0 , 0 , 0 , 0 , 0\r\ngwas_all_chrpos.size():4,913\r\ncount_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based:    153 , 280 , 153 , 160 , 4,912 , 172\r\nwhich_build_gwas,which_build_ref:       hg19_1 , unknown\r\nssimp-linux-0.3: src/ssimp.cc:713: int main(int, char**): Assertion `which_build_ref != ssimp:: which_build_t:: unknown' failed.\r\nAborted (core dumped)\r\n```\r\n\r\nDoes the program think there are some SNPs on hg20? But this is definitely not the case. Moreover, I've ensured that all SNP IDs, positions and alleles in my GWAS file match those in the reference panel VCF.\r\n\r\nAny help would be very much appreciated. Thank-you!\r\n\r\nJimmy"},"comment":{"url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/comments/440242366","html_url":"https://github.com/zkutalik/ssimp_software/issues/61#issuecomment-440242366","issue_url":"https://api.github.com/repos/zkutalik/ssimp_software/issues/61","id":440242366,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MDI0MjM2Ng==","user":{"login":"zkutalik","id":15266485,"node_id":"MDQ6VXNlcjE1MjY2NDg1","avatar_url":"https://avatars3.githubusercontent.com/u/15266485?v=4","gravatar_id":"","url":"https://api.github.com/users/zkutalik","html_url":"https://github.com/zkutalik","followers_url":"https://api.github.com/users/zkutalik/followers","following_url":"https://api.github.com/users/zkutalik/following{/other_user}","gists_url":"https://api.github.com/users/zkutalik/gists{/gist_id}","starred_url":"https://api.github.com/users/zkutalik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zkutalik/subscriptions","organizations_url":"https://api.github.com/users/zkutalik/orgs","repos_url":"https://api.github.com/users/zkutalik/repos","events_url":"https://api.github.com/users/zkutalik/events{/privacy}","received_events_url":"https://api.github.com/users/zkutalik/received_events","type":"User","site_admin":false},"created_at":"2018-11-20T11:34:42Z","updated_at":"2018-11-20T11:34:42Z","author_association":"OWNER","body":"Good point, with increasing ref panel size, the problem becomes more burning. UKB data has been imputed to ~100M variants - so there it shouldn't be an issue."}}
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