payload: {"action":"closed","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/1141","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/1141/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/1141/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/1141/events","html_url":"https://github.com/samtools/bcftools/issues/1141","id":548255395,"node_id":"MDU6SXNzdWU1NDgyNTUzOTU=","number":1141,"title":"bcftools mpileup 1.10.2 no longer has \"dummy VCF creation\" functionality","user":{"login":"ahstram","id":9671536,"node_id":"MDQ6VXNlcjk2NzE1MzY=","avatar_url":"https://avatars3.githubusercontent.com/u/9671536?v=4","gravatar_id":"","url":"https://api.github.com/users/ahstram","html_url":"https://github.com/ahstram","followers_url":"https://api.github.com/users/ahstram/followers","following_url":"https://api.github.com/users/ahstram/following{/other_user}","gists_url":"https://api.github.com/users/ahstram/gists{/gist_id}","starred_url":"https://api.github.com/users/ahstram/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ahstram/subscriptions","organizations_url":"https://api.github.com/users/ahstram/orgs","repos_url":"https://api.github.com/users/ahstram/repos","events_url":"https://api.github.com/users/ahstram/events{/privacy}","received_events_url":"https://api.github.com/users/ahstram/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2020-01-10T19:39:58Z","updated_at":"2020-01-10T21:50:53Z","closed_at":"2020-01-10T21:50:53Z","author_association":"NONE","body":"Hi there,\r\n\r\nI'm not sure if this was intentional, but bcftools version 1.9 had a nice ability to create a \"dummy\" empty VCF, which I could do with this command:\r\n\r\n`bcftools mpileup - --no-reference <<< \"\"`\r\n\r\nbcftools would then create a \"dummy\" VCF file with no records, but sufficient header information such that I could then pass this empty VCF file to a command like \"bcftools concat\" without running into an error about a malformed VCF header, which will happen with an empty file.\r\n\r\nThe significance of creating a \"dummy\" VCF is to act as a placeholder for analyses that did not produce results (no variants called), but later steps in our pipelines still expect a well-formed VCF file to operate on (for steps such as \"bcftools concat\").\r\n\r\nIt seems that with bcftools 1.10.2, running the command `bcftools mpileup - --no-reference <<< \"\"` now results in an error message:\r\n\r\n> [mpileup] fail to read the header of -\r\n\r\nWould it be possible to bring back the \"dummy VCF creation\" functionality which existed in bcftools v1.9 by running the command `bcftools mpileup - --no-reference <<< \"\"`?\r\n\r\nThank you,\r\n\r\nAlex"}}
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