{"action":"created","issue":{"url":"https://api.github.com/repos/genometools/genometools/issues/696","labels_url":"https://api.github.com/repos/genometools/genometools/issues/696/labels{/name}","comments_url":"https://api.github.com/repos/genometools/genometools/issues/696/comments","events_url":"https://api.github.com/repos/genometools/genometools/issues/696/events","html_url":"https://github.com/genometools/genometools/issues/696","id":118531328,"number":696,"title":"gt gff3 -checkids","user":{"login":"agolicz","id":10213846,"avatar_url":"https://avatars.githubusercontent.com/u/10213846?v=3","gravatar_id":"","url":"https://api.github.com/users/agolicz","html_url":"https://github.com/agolicz","followers_url":"https://api.github.com/users/agolicz/followers","following_url":"https://api.github.com/users/agolicz/following{/other_user}","gists_url":"https://api.github.com/users/agolicz/gists{/gist_id}","starred_url":"https://api.github.com/users/agolicz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agolicz/subscriptions","organizations_url":"https://api.github.com/users/agolicz/orgs","repos_url":"https://api.github.com/users/agolicz/repos","events_url":"https://api.github.com/users/agolicz/events{/privacy}","received_events_url":"https://api.github.com/users/agolicz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-24T04:54:37Z","updated_at":"2015-11-27T00:52:19Z","closed_at":null,"body":"Hello,\r\n\r\nI have a bit of a problem with gt gff3, I wanted to check if I have duplicate gene ids in my file, but the flag seems not to be working.\r\n\r\nAfter gt gff3 -sort yes -retainids yes -checkids yes test.gff3 > gt.out.gff3\r\n\r\n[gt.out.gff3.txt](https://github.com/genometools/genometools/files/42371/gt.out.gff3.txt)\r\n[test.gff3.txt](https://github.com/genometools/genometools/files/42372/test.gff3.txt)\r\n\r\nThere is no warning about duplicate gene ids although they are present. The duplicate gene gets grouped with the first gene.  I tested v1.5.7 and v.1.5.4\r\nIs that expected behavior? It seems counter-intuitive.\r\n\r\nI also have a historical question. I was trying to re-run some analysis from 2012. Back then I used v.1.3.5 and I used to get warnings:\r\nwarning: feature ID \"BOLE_PAN00005191.1:cds\" not unique: changing to BOLE_PAN00005191.1:cds.1\r\n\r\nBut what I did not notice is that for some genes the ids got changed and for the others not.\r\n\r\nSo I ended up with a mosaic file which looked like this: \r\n[historical.mosaic.gff3.txt](https://github.com/genometools/genometools/files/42373/historical.mosaic.gff3.txt)\r\n \r\nAny idea what could have caused that back then? It seems bizarre. It is important \r\nfor my re-analysis as I am trying to understand if it was a strange gff3 file or unexpected \r\nprogram behavior. Again no errors.\r\n\r\nBest wishes,\r\nAgnieszka\r\n"},"comment":{"url":"https://api.github.com/repos/genometools/genometools/issues/comments/160012469","html_url":"https://github.com/genometools/genometools/issues/696#issuecomment-160012469","issue_url":"https://api.github.com/repos/genometools/genometools/issues/696","id":160012469,"user":{"login":"gordon","id":6835,"avatar_url":"https://avatars.githubusercontent.com/u/6835?v=3","gravatar_id":"","url":"https://api.github.com/users/gordon","html_url":"https://github.com/gordon","followers_url":"https://api.github.com/users/gordon/followers","following_url":"https://api.github.com/users/gordon/following{/other_user}","gists_url":"https://api.github.com/users/gordon/gists{/gist_id}","starred_url":"https://api.github.com/users/gordon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gordon/subscriptions","organizations_url":"https://api.github.com/users/gordon/orgs","repos_url":"https://api.github.com/users/gordon/repos","events_url":"https://api.github.com/users/gordon/events{/privacy}","received_events_url":"https://api.github.com/users/gordon/received_events","type":"User","site_admin":false},"created_at":"2015-11-27T00:52:19Z","updated_at":"2015-11-27T00:52:19Z","body":"It seems that you did copy&paste with your files, they do not contain any tabs anymore.\r\n\r\nConcerning your first problem: That's probably due to the fact that we relaxed a check in commit 20efc5c7dc0d47fc5437cbab846c072ac4b00f75 to fix issue #153.\r\nThat means that your two genes are now considered as a multi-feature. The GFF3 specification says:\r\n\r\n> ID\r\n> Indicates the ID of the feature. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature.\r\n\r\nIf the genes would be separated by a `###` line the parser would throw an error, but since they are not they are considered now a multi-feature. I agree that it is seems counter-intuitive in your case, but changing it back to the old behaviour would break cases like the one described in issue #153 which are within the specification. If the example file was concatenated by you, make sure you add `###` lines. If it was produced like that by the software you used you could file a bug report upstream.\r\n\r\nConcerning your second problem: This might be related to the same code change as above or be due to some bugs we fixed in the meantime. Unfortunately, we cannot support old releases of GenomeTools. You could dig through old issues and commits yourself to figure out what changed. If you can produce an imput file which produces an error in the current version of GenomeTools we'll look into it, though. Sorry."}}