{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/520","repository_url":"https://api.github.com/repos/fidelram/deepTools","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/520/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/520/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/520/events","html_url":"https://github.com/fidelram/deepTools/issues/520","id":224250859,"number":520,"title":"bamCoverage --filterRNAstrand doesn't respect --extendReads","user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars0.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"labels":[{"id":46870946,"url":"https://api.github.com/repos/fidelram/deepTools/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars0.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"assignees":[{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars0.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/fidelram/deepTools/milestones/9","html_url":"https://github.com/fidelram/deepTools/milestone/9","labels_url":"https://api.github.com/repos/fidelram/deepTools/milestones/9/labels","id":2474991,"number":9,"title":"2.5.1","description":"Bug fixes on the 2.5.0 release.","creator":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars0.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":3,"state":"open","created_at":"2017-04-23T18:54:28Z","updated_at":"2017-04-26T13:00:15Z","due_on":null,"closed_at":null},"comments":0,"created_at":"2017-04-25T19:44:37Z","updated_at":"2017-04-26T13:24:54Z","closed_at":null,"body":"From the mailing list, it turns out that `bamCoverage --filterRNAstrand something` will ignore `--extendReads`. This can be fixed by adding `--Offset 1 -1`, which was quite clever on the part of the person who submitted the report, but that shouldn't be needed.\r\n\r\nThere are two good fixes:\r\n\r\n1. Add support for read extension to the `filterRNAstrand` class.\r\n2. Check for `--filterRNAstrand` and set `--Offset` to `[1, -1]` in such cases. This has the benefit of reducing the amount of code that needs maintaining."},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/297406784","html_url":"https://github.com/fidelram/deepTools/issues/520#issuecomment-297406784","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/520","id":297406784,"user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars0.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"created_at":"2017-04-26T13:24:54Z","updated_at":"2017-04-26T13:24:54Z","body":"I'm going to go with option 2, since that decreases the overall amount of code :)"}}
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