{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/413","repository_url":"https://api.github.com/repos/fidelram/deepTools","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/413/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/413/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/413/events","html_url":"https://github.com/fidelram/deepTools/issues/413","id":174395636,"number":413,"title":"--nanAfterEnd doesn't always work properly","user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars.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":[{"url":"https://api.github.com/repos/fidelram/deepTools/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars.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://avatars.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":null,"comments":0,"created_at":"2016-08-31T22:36:21Z","updated_at":"2016-09-02T08:52:07Z","closed_at":null,"body":"This was reported via Galaxy. The `--nanAfterEnd` option doesn't always work properly in computeMatrix. Since integer math is use, we can end up having one too few bins on either side. One way to fix that might be:\r\n\r\n    if padLeftNaN > 0:\r\n        expected = parameters['upstream'] // parameters['bin size']\r\n        padLeftNaN = int(round(float(padLeftNaN) / parameters['bin size']))\r\n        if expected - padLeftNaN - a > 0:\r\n            padLeftNaN += 1\r\n    if padRightNaN > 0:\r\n        expected = parameters['downstream'] // parameters['bin size']\r\n        padRightNaN = int(round(float(padRightNaN) / parameters['bin size']))\r\n        if expected - padRightNaN - e > 0:\r\n            padRightNaN += 1\r\n\r\nI'm not entirely sure yet that this is doing the proper thing, but at least things don't crash."},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/244319885","html_url":"https://github.com/fidelram/deepTools/issues/413#issuecomment-244319885","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/413","id":244319885,"user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars.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":"2016-09-02T08:52:07Z","updated_at":"2016-09-02T08:52:07Z","body":"Right, while padLeftNaN and padRightNaN are correct according to the strand, the upstream/downstream values aren't, so that needs to be taken into account too."}}
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