{"action":"created","issue":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/15","labels_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/15/comments","events_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/15/events","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/15","id":105081508,"number":15,"title":"ValueError quality and sequence mismatch: 76 != 59","user":{"login":"nordhuang","id":5283165,"avatar_url":"https://avatars.githubusercontent.com/u/5283165?v=3","gravatar_id":"","url":"https://api.github.com/users/nordhuang","html_url":"https://github.com/nordhuang","followers_url":"https://api.github.com/users/nordhuang/followers","following_url":"https://api.github.com/users/nordhuang/following{/other_user}","gists_url":"https://api.github.com/users/nordhuang/gists{/gist_id}","starred_url":"https://api.github.com/users/nordhuang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nordhuang/subscriptions","organizations_url":"https://api.github.com/users/nordhuang/orgs","repos_url":"https://api.github.com/users/nordhuang/repos","events_url":"https://api.github.com/users/nordhuang/events{/privacy}","received_events_url":"https://api.github.com/users/nordhuang/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-09-06T09:18:54Z","updated_at":"2015-09-06T17:12:59Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/pulls/15","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/15","diff_url":"https://github.com/loeblab/Duplex-Sequencing/pull/15.diff","patch_url":"https://github.com/loeblab/Duplex-Sequencing/pull/15.patch"},"body":"File \"pysam/calignmentfile.pyx\", line 2775, in pysam.calignmentfile.AlignedSegment.query_qualities.__set__ (pysam/calignmentfile.c:29387)\r\nValueError: quality and sequence mismatch: 76 != 59"},"comment":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/comments/138100917","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/15#issuecomment-138100917","issue_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/15","id":138100917,"user":{"login":"loeblab","id":2035536,"avatar_url":"https://avatars.githubusercontent.com/u/2035536?v=3","gravatar_id":"","url":"https://api.github.com/users/loeblab","html_url":"https://github.com/loeblab","followers_url":"https://api.github.com/users/loeblab/followers","following_url":"https://api.github.com/users/loeblab/following{/other_user}","gists_url":"https://api.github.com/users/loeblab/gists{/gist_id}","starred_url":"https://api.github.com/users/loeblab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/loeblab/subscriptions","organizations_url":"https://api.github.com/users/loeblab/orgs","repos_url":"https://api.github.com/users/loeblab/repos","events_url":"https://api.github.com/users/loeblab/events{/privacy}","received_events_url":"https://api.github.com/users/loeblab/received_events","type":"User","site_admin":false},"created_at":"2015-09-06T17:12:59Z","updated_at":"2015-09-06T17:12:59Z","body":"I get what you're trying to do, but this seems like a case of either a malformed bam file or you're telling the program that your read lengths are longer than they actually are when you put in the parameters when running ConsensusMaker.py.  If you can demonstrate that neither is true, then that would be bug and I'm willing to entertain a solution."}}