{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/315","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/315/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/315/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/315/events","html_url":"https://github.com/samtools/bcftools/pull/315","id":104613027,"number":315,"title":"Add test for splitting and merging in one go","user":{"login":"jpiper","id":986448,"avatar_url":"https://avatars.githubusercontent.com/u/986448?v=3","gravatar_id":"","url":"https://api.github.com/users/jpiper","html_url":"https://github.com/jpiper","followers_url":"https://api.github.com/users/jpiper/followers","following_url":"https://api.github.com/users/jpiper/following{/other_user}","gists_url":"https://api.github.com/users/jpiper/gists{/gist_id}","starred_url":"https://api.github.com/users/jpiper/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpiper/subscriptions","organizations_url":"https://api.github.com/users/jpiper/orgs","repos_url":"https://api.github.com/users/jpiper/repos","events_url":"https://api.github.com/users/jpiper/events{/privacy}","received_events_url":"https://api.github.com/users/jpiper/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-09-03T03:19:35Z","updated_at":"2015-09-03T11:12:23Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/samtools/bcftools/pulls/315","html_url":"https://github.com/samtools/bcftools/pull/315","diff_url":"https://github.com/samtools/bcftools/pull/315.diff","patch_url":"https://github.com/samtools/bcftools/pull/315.patch"},"body":"I saw that support for for splitting and normalising in one go was introduced in c982c86a7b8fdcd4beff9bb3f7a4fc77e88f0d1a\r\n\r\nBut there has been no test created for this. I created the `norm.split.and.norm.out` test output with\r\n\r\n```\r\n$ ../bcftools norm -m- norm.split.vcf > temp.vcf\r\n$ ../bcftools norm -f norm.fa temp.vcf | grep -v '^##bcftools_' > norm.split.and.norm.out\r\n$ rm temp.vcf\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/bcftools/issues/comments/137409970","html_url":"https://github.com/samtools/bcftools/pull/315#issuecomment-137409970","issue_url":"https://api.github.com/repos/samtools/bcftools/issues/315","id":137409970,"user":{"login":"jpiper","id":986448,"avatar_url":"https://avatars.githubusercontent.com/u/986448?v=3","gravatar_id":"","url":"https://api.github.com/users/jpiper","html_url":"https://github.com/jpiper","followers_url":"https://api.github.com/users/jpiper/followers","following_url":"https://api.github.com/users/jpiper/following{/other_user}","gists_url":"https://api.github.com/users/jpiper/gists{/gist_id}","starred_url":"https://api.github.com/users/jpiper/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpiper/subscriptions","organizations_url":"https://api.github.com/users/jpiper/orgs","repos_url":"https://api.github.com/users/jpiper/repos","events_url":"https://api.github.com/users/jpiper/events{/privacy}","received_events_url":"https://api.github.com/users/jpiper/received_events","type":"User","site_admin":false},"created_at":"2015-09-03T11:12:23Z","updated_at":"2015-09-03T11:12:23Z","body":"I can also confirm that this bug exists using  `Version: 1.2 (using htslib 1.2.1)`\r\n\r\n    $ bcftools norm -m- norm.split.vcf | bcftools norm -f norm.fa\r\n\r\nreturns\r\n\r\n    2\t101\t.\tA\tATT\t999\tPASS\tINDEL;AN=4;AC=4\tGT:DP\t1/1:1\t1/1:1\r\n    2\t101\t.\tA\tAT\t999\tPASS\tINDEL;AN=4;AC=2\tGT:DP\t0/1:1\t0/1:1"}}