{"action":"created","issue":{"url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/1","labels_url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/1/comments","events_url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/1/events","html_url":"https://github.com/cbrueffer/tophat-recondition/issues/1","id":97698724,"number":1,"title":"\"Mapped mate should have mate reference name\" problem","user":{"login":"drchriscole","id":6098785,"avatar_url":"https://avatars.githubusercontent.com/u/6098785?v=3","gravatar_id":"","url":"https://api.github.com/users/drchriscole","html_url":"https://github.com/drchriscole","followers_url":"https://api.github.com/users/drchriscole/followers","following_url":"https://api.github.com/users/drchriscole/following{/other_user}","gists_url":"https://api.github.com/users/drchriscole/gists{/gist_id}","starred_url":"https://api.github.com/users/drchriscole/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drchriscole/subscriptions","organizations_url":"https://api.github.com/users/drchriscole/orgs","repos_url":"https://api.github.com/users/drchriscole/repos","events_url":"https://api.github.com/users/drchriscole/events{/privacy}","received_events_url":"https://api.github.com/users/drchriscole/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-07-28T12:50:28Z","updated_at":"2015-08-12T16:28:35Z","closed_at":null,"body":"Hi,\r\n\r\nReally liking your tool, it should make submitting my BAMs to ENA much simpler. However, I'm getting the error above and have exactly the same features 'id0' does in the SeqAnswers thread. e.g. offending read is only in unmapped.bam and the MAPQ is changed from 255 to 0 by your script.\r\n\r\nI'm not using any special settings in TopHat (v2.0.9), only -i to adjust intron size.\r\nDo you have any suggestions for getting around it, please?\r\nThanks,\r\n\r\nChris"},"comment":{"url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/comments/130362809","html_url":"https://github.com/cbrueffer/tophat-recondition/issues/1#issuecomment-130362809","issue_url":"https://api.github.com/repos/cbrueffer/tophat-recondition/issues/1","id":130362809,"user":{"login":"drchriscole","id":6098785,"avatar_url":"https://avatars.githubusercontent.com/u/6098785?v=3","gravatar_id":"","url":"https://api.github.com/users/drchriscole","html_url":"https://github.com/drchriscole","followers_url":"https://api.github.com/users/drchriscole/followers","following_url":"https://api.github.com/users/drchriscole/following{/other_user}","gists_url":"https://api.github.com/users/drchriscole/gists{/gist_id}","starred_url":"https://api.github.com/users/drchriscole/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drchriscole/subscriptions","organizations_url":"https://api.github.com/users/drchriscole/orgs","repos_url":"https://api.github.com/users/drchriscole/repos","events_url":"https://api.github.com/users/drchriscole/events{/privacy}","received_events_url":"https://api.github.com/users/drchriscole/received_events","type":"User","site_admin":false},"created_at":"2015-08-12T16:28:35Z","updated_at":"2015-08-12T16:28:35Z","body":"Running with the LENIENT flag reveals lots of reads with this problem."}}