{"action":"created","issue":{"url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/31","labels_url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/31/comments","events_url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/31/events","html_url":"https://github.com/pjotrp/bioruby-vcf/issues/31","id":113582855,"number":31,"title":"Change delimiter for lists","user":{"login":"mjafin","id":3286525,"avatar_url":"https://avatars.githubusercontent.com/u/3286525?v=3","gravatar_id":"","url":"https://api.github.com/users/mjafin","html_url":"https://github.com/mjafin","followers_url":"https://api.github.com/users/mjafin/followers","following_url":"https://api.github.com/users/mjafin/following{/other_user}","gists_url":"https://api.github.com/users/mjafin/gists{/gist_id}","starred_url":"https://api.github.com/users/mjafin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjafin/subscriptions","organizations_url":"https://api.github.com/users/mjafin/orgs","repos_url":"https://api.github.com/users/mjafin/repos","events_url":"https://api.github.com/users/mjafin/events{/privacy}","received_events_url":"https://api.github.com/users/mjafin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-27T13:27:10Z","updated_at":"2015-10-28T20:15:50Z","closed_at":null,"body":"Hi there,\r\nThanks for bio-vcf, I've found it incredibly useful and fast. I may be missing something, but when I'm using tab-delimited output I sometimes have fields that can have zero, one or more comma delimited values, like for example under `ANN`. It looks like these are automatically tab-delimited in the output and therefore I can't predict the number of columns on each line ahead. Is there a way to change this behaviour so that within field delimiter would be, say, comma?"},"comment":{"url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/comments/151977267","html_url":"https://github.com/pjotrp/bioruby-vcf/issues/31#issuecomment-151977267","issue_url":"https://api.github.com/repos/pjotrp/bioruby-vcf/issues/31","id":151977267,"user":{"login":"mjafin","id":3286525,"avatar_url":"https://avatars.githubusercontent.com/u/3286525?v=3","gravatar_id":"","url":"https://api.github.com/users/mjafin","html_url":"https://github.com/mjafin","followers_url":"https://api.github.com/users/mjafin/followers","following_url":"https://api.github.com/users/mjafin/following{/other_user}","gists_url":"https://api.github.com/users/mjafin/gists{/gist_id}","starred_url":"https://api.github.com/users/mjafin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjafin/subscriptions","organizations_url":"https://api.github.com/users/mjafin/orgs","repos_url":"https://api.github.com/users/mjafin/repos","events_url":"https://api.github.com/users/mjafin/events{/privacy}","received_events_url":"https://api.github.com/users/mjafin/received_events","type":"User","site_admin":false},"created_at":"2015-10-28T20:15:50Z","updated_at":"2015-10-28T20:15:50Z","body":"Hi @pjotrp, thanks for looking into this, happy to provide an example. Say I wanted to get tab-delimited output from vcf in the following way:\r\n`zcat my.vcf.gz | bio-vcf --sfilter 'rec.filter==\"PASS\"' --eval '[r.chr,r.ref,r.alt,r.info.svtype,r.info.end,r.info.known,r.info.lof,r.info.simple_ann]' --seval '[s.pr]'`\r\n\r\nThen if all the fields contain one value, I'll have 9 columns. However, if e.g. the `KNOWN` field contains more than one value, separated by commas, there'll be more than 9 columns on those lines. In our case `KNOWN` is a list of genes affected by a structural variant. I'd like to have them comma separated in the tab-delimited output rather than tab-delimited within tab-delimited if that makes sense."}}