{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/401","repository_url":"https://api.github.com/repos/arq5x/bedtools2","labels_url":"https://api.github.com/repos/arq5x/bedtools2/issues/401/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/bedtools2/issues/401/comments","events_url":"https://api.github.com/repos/arq5x/bedtools2/issues/401/events","html_url":"https://github.com/arq5x/bedtools2/issues/401","id":152862909,"number":401,"title":"bedtools complement outputs invalid bed file when input covers entire chromosome","user":{"login":"dvera","id":5902410,"avatar_url":"https://avatars.githubusercontent.com/u/5902410?v=3","gravatar_id":"","url":"https://api.github.com/users/dvera","html_url":"https://github.com/dvera","followers_url":"https://api.github.com/users/dvera/followers","following_url":"https://api.github.com/users/dvera/following{/other_user}","gists_url":"https://api.github.com/users/dvera/gists{/gist_id}","starred_url":"https://api.github.com/users/dvera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dvera/subscriptions","organizations_url":"https://api.github.com/users/dvera/orgs","repos_url":"https://api.github.com/users/dvera/repos","events_url":"https://api.github.com/users/dvera/events{/privacy}","received_events_url":"https://api.github.com/users/dvera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-03T20:08:23Z","updated_at":"2016-05-03T20:09:40Z","closed_at":null,"body":"bedtools complement outputs a bed file with coordinates 0 0 when the input covers an entire chromosome. Perhaps nothing should be printed in that case so the files are browser-compliant?\r\n\r\necho -e 'chr1\\t0\\t249250621' > test.bed\r\nbedtools complement -i test.bed -g hg19.chrom.sizes\r\nchr1\t0\t0\r\nchr10\t1\t135534746\r\nchr11\t0\t135006516\r\nchr12\t0\t133851895\r\nchr13\t0\t115169878\r\nchr14\t0\t107349540\r\nchr15\t0\t102531392\r\nchr16\t0\t90354753\r\nchr17\t0\t81195210\r\nchr18\t0\t78077248\r\nchr19\t0\t59128983\r\nchr2\t0\t243199373\r\nchr20\t0\t63025520\r\nchr21\t0\t48129895\r\nchr22\t0\t51304566\r\nchr3\t0\t198022430\r\nchr4\t0\t191154276\r\nchr5\t0\t180915260\r\nchr6\t0\t171115067\r\nchr7\t0\t159138663\r\nchr8\t0\t146364022\r\nchr9\t0\t141213431\r\nchrM\t0\t16571\r\nchrX\t0\t155270560\r\nchrY\t0\t59373566"},"comment":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/comments/216649970","html_url":"https://github.com/arq5x/bedtools2/issues/401#issuecomment-216649970","issue_url":"https://api.github.com/repos/arq5x/bedtools2/issues/401","id":216649970,"user":{"login":"dvera","id":5902410,"avatar_url":"https://avatars.githubusercontent.com/u/5902410?v=3","gravatar_id":"","url":"https://api.github.com/users/dvera","html_url":"https://github.com/dvera","followers_url":"https://api.github.com/users/dvera/followers","following_url":"https://api.github.com/users/dvera/following{/other_user}","gists_url":"https://api.github.com/users/dvera/gists{/gist_id}","starred_url":"https://api.github.com/users/dvera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dvera/subscriptions","organizations_url":"https://api.github.com/users/dvera/orgs","repos_url":"https://api.github.com/users/dvera/repos","events_url":"https://api.github.com/users/dvera/events{/privacy}","received_events_url":"https://api.github.com/users/dvera/received_events","type":"User","site_admin":false},"created_at":"2016-05-03T20:09:40Z","updated_at":"2016-05-03T20:09:40Z","body":"Also just realized chr10 has a start of 1 instead of 0."}}