{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/server/issues/433","labels_url":"https://api.github.com/repos/ga4gh/server/issues/433/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/server/issues/433/comments","events_url":"https://api.github.com/repos/ga4gh/server/issues/433/events","html_url":"https://github.com/ga4gh/server/issues/433","id":84215388,"number":433,"title":"this query get wrong server response back.","user":{"login":"jingchunzhu","id":999493,"avatar_url":"https://avatars.githubusercontent.com/u/999493?v=3","gravatar_id":"","url":"https://api.github.com/users/jingchunzhu","html_url":"https://github.com/jingchunzhu","followers_url":"https://api.github.com/users/jingchunzhu/followers","following_url":"https://api.github.com/users/jingchunzhu/following{/other_user}","gists_url":"https://api.github.com/users/jingchunzhu/gists{/gist_id}","starred_url":"https://api.github.com/users/jingchunzhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jingchunzhu/subscriptions","organizations_url":"https://api.github.com/users/jingchunzhu/orgs","repos_url":"https://api.github.com/users/jingchunzhu/repos","events_url":"https://api.github.com/users/jingchunzhu/events{/privacy}","received_events_url":"https://api.github.com/users/jingchunzhu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"dcolligan","id":7422120,"avatar_url":"https://avatars.githubusercontent.com/u/7422120?v=3","gravatar_id":"","url":"https://api.github.com/users/dcolligan","html_url":"https://github.com/dcolligan","followers_url":"https://api.github.com/users/dcolligan/followers","following_url":"https://api.github.com/users/dcolligan/following{/other_user}","gists_url":"https://api.github.com/users/dcolligan/gists{/gist_id}","starred_url":"https://api.github.com/users/dcolligan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcolligan/subscriptions","organizations_url":"https://api.github.com/users/dcolligan/orgs","repos_url":"https://api.github.com/users/dcolligan/repos","events_url":"https://api.github.com/users/dcolligan/events{/privacy}","received_events_url":"https://api.github.com/users/dcolligan/received_events","type":"User","site_admin":false},"milestone":null,"comments":19,"created_at":"2015-06-02T21:17:26Z","updated_at":"2015-06-15T21:11:49Z","closed_at":null,"body":"This following query against umd get 2520 variants back, many are not within the start and end interval\r\npython client_dev.py -vv variants-search --variantSetIds umd --referenceName 17 --start 41227747  --end 41244748 --pageSize 1000 http://ec2-54-148-207-224.us-west-2.compute.amazonaws.com:8000/v0.6.e6d6074\r\n2520 variants\r\n\r\nThe most strange thing is that the xena browser client (in javascript) also get the \"same\"(same in the sense that the same number of variants returned) wrong answer back.\r\n\r\nhowever,  curl command seems to get the correct response back.\r\n\r\ncurl --data '{ \"callSetIds\": [],  \"end\": 41244748, \"referenceName\": \"17\",  \"start\":41227747,  \"variantSetIds\": [\"umd”], “pageSize”:1000}’ --header 'Content-Type: application/json' http://ec2-54-148-207-224.us-west-2.compute.amazonaws.com:8000/v0.6.e6d6074/variants/search\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ga4gh/server/issues/comments/112213423","html_url":"https://github.com/ga4gh/server/issues/433#issuecomment-112213423","issue_url":"https://api.github.com/repos/ga4gh/server/issues/433","id":112213423,"user":{"login":"dcolligan","id":7422120,"avatar_url":"https://avatars.githubusercontent.com/u/7422120?v=3","gravatar_id":"","url":"https://api.github.com/users/dcolligan","html_url":"https://github.com/dcolligan","followers_url":"https://api.github.com/users/dcolligan/followers","following_url":"https://api.github.com/users/dcolligan/following{/other_user}","gists_url":"https://api.github.com/users/dcolligan/gists{/gist_id}","starred_url":"https://api.github.com/users/dcolligan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcolligan/subscriptions","organizations_url":"https://api.github.com/users/dcolligan/orgs","repos_url":"https://api.github.com/users/dcolligan/repos","events_url":"https://api.github.com/users/dcolligan/events{/privacy}","received_events_url":"https://api.github.com/users/dcolligan/received_events","type":"User","site_admin":false},"created_at":"2015-06-15T21:11:49Z","updated_at":"2015-06-15T21:11:49Z","body":"For this particular query, it looks like 529 out of 2520 variants returned to the client are defective, all because the start and end of the returned variant are less than the request's start attribute.  It looks like a problem with the paging code, as 1991 variants are returned by the lower-level query to `HtslibVariantSet.getVariants` (and none of those have start and end less than `startPosition`).  Continuing to investigate..."}}