{"action":"opened","issue":{"url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/44","repository_url":"https://api.github.com/repos/opencb/hpg-bigdata","labels_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/44/labels{/name}","comments_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/44/comments","events_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/44/events","html_url":"https://github.com/opencb/hpg-bigdata/issues/44","id":169166170,"number":44,"title":"Improve 'variant convert' command line","user":{"login":"jtarraga","id":1344034,"avatar_url":"https://avatars.githubusercontent.com/u/1344034?v=3","gravatar_id":"","url":"https://api.github.com/users/jtarraga","html_url":"https://github.com/jtarraga","followers_url":"https://api.github.com/users/jtarraga/followers","following_url":"https://api.github.com/users/jtarraga/following{/other_user}","gists_url":"https://api.github.com/users/jtarraga/gists{/gist_id}","starred_url":"https://api.github.com/users/jtarraga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jtarraga/subscriptions","organizations_url":"https://api.github.com/users/jtarraga/orgs","repos_url":"https://api.github.com/users/jtarraga/repos","events_url":"https://api.github.com/users/jtarraga/events{/privacy}","received_events_url":"https://api.github.com/users/jtarraga/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/opencb/hpg-bigdata/labels/task","name":"task","color":"eb6420"}],"state":"open","locked":false,"assignee":{"login":"jtarraga","id":1344034,"avatar_url":"https://avatars.githubusercontent.com/u/1344034?v=3","gravatar_id":"","url":"https://api.github.com/users/jtarraga","html_url":"https://github.com/jtarraga","followers_url":"https://api.github.com/users/jtarraga/followers","following_url":"https://api.github.com/users/jtarraga/following{/other_user}","gists_url":"https://api.github.com/users/jtarraga/gists{/gist_id}","starred_url":"https://api.github.com/users/jtarraga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jtarraga/subscriptions","organizations_url":"https://api.github.com/users/jtarraga/orgs","repos_url":"https://api.github.com/users/jtarraga/repos","events_url":"https://api.github.com/users/jtarraga/events{/privacy}","received_events_url":"https://api.github.com/users/jtarraga/received_events","type":"User","site_admin":false},"assignees":[{"login":"jtarraga","id":1344034,"avatar_url":"https://avatars.githubusercontent.com/u/1344034?v=3","gravatar_id":"","url":"https://api.github.com/users/jtarraga","html_url":"https://github.com/jtarraga","followers_url":"https://api.github.com/users/jtarraga/followers","following_url":"https://api.github.com/users/jtarraga/following{/other_user}","gists_url":"https://api.github.com/users/jtarraga/gists{/gist_id}","starred_url":"https://api.github.com/users/jtarraga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jtarraga/subscriptions","organizations_url":"https://api.github.com/users/jtarraga/orgs","repos_url":"https://api.github.com/users/jtarraga/repos","events_url":"https://api.github.com/users/jtarraga/events{/privacy}","received_events_url":"https://api.github.com/users/jtarraga/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/opencb/hpg-bigdata/milestones/5","html_url":"https://github.com/opencb/hpg-bigdata/milestones/v1.0.0-alpha","labels_url":"https://api.github.com/repos/opencb/hpg-bigdata/milestones/5/labels","id":1915770,"number":5,"title":"v1.0.0-alpha","description":"","creator":{"login":"imedina","id":1427327,"avatar_url":"https://avatars.githubusercontent.com/u/1427327?v=3","gravatar_id":"","url":"https://api.github.com/users/imedina","html_url":"https://github.com/imedina","followers_url":"https://api.github.com/users/imedina/followers","following_url":"https://api.github.com/users/imedina/following{/other_user}","gists_url":"https://api.github.com/users/imedina/gists{/gist_id}","starred_url":"https://api.github.com/users/imedina/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/imedina/subscriptions","organizations_url":"https://api.github.com/users/imedina/orgs","repos_url":"https://api.github.com/users/imedina/repos","events_url":"https://api.github.com/users/imedina/events{/privacy}","received_events_url":"https://api.github.com/users/imedina/received_events","type":"User","site_admin":false},"open_issues":6,"closed_issues":0,"state":"open","created_at":"2016-08-01T13:28:28Z","updated_at":"2016-08-03T15:49:46Z","due_on":"2016-08-30T23:00:00Z","closed_at":null},"comments":0,"created_at":"2016-08-03T15:49:46Z","updated_at":"2016-08-03T15:49:46Z","closed_at":null,"body":"Currently, the 'variant convert' command line contains '--to-avro', '--to-parquet', '--to-json',... parameters, they can be grouped in one parameter --to {avro | parquet | json}. In addition, the command line should offer some basic filters (e.g., region filter, quality filter,...) and it lacks of some important Parquet parameters (e.g. page size, row group size) to take into account:\r\n\r\n./hpg-bigdata.sh variant convert -i .... -o .... --to {avro | parquet | json} [--from {vcf|avro}]  --compression {deflate | snappy | ...}  --data-model {opencb|ga4gh}  [--page-size ...]  [--row-group-size ...]  [--include-formats ....] [--region ....]  [--region-file ....]  [--qual ....]  [--filter ....] [--only-with-id] \r\n\r\n"}}
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