{"action":"created","issue":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/31","repository_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing","labels_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/31/comments","events_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/31/events","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/31","id":148220583,"number":31,"title":"Flag should be 5 for unpaired reads (they are still paired, just this…","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-14T00:52:59Z","updated_at":"2016-04-14T15:15:09Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/pulls/31","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/31","diff_url":"https://github.com/loeblab/Duplex-Sequencing/pull/31.diff","patch_url":"https://github.com/loeblab/Duplex-Sequencing/pull/31.patch"},"body":"… end of the pair is unmapped)"},"comment":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/comments/209995853","html_url":"https://github.com/loeblab/Duplex-Sequencing/pull/31#issuecomment-209995853","issue_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/31","id":209995853,"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":"2016-04-14T15:15:09Z","updated_at":"2016-04-14T15:15:09Z","body":"So this is a bit tough. Most of the info in the final dcs.bam file is just dummy information. We regenerate the FLAGS and CIGAR strings by realigning the final dcs reads, which then just recomputes all of these values based on this new alignment.  The old values really have little to no meaning because the underlying sequence has been modified during the consensus making (insertion of N's, etc). Why did I do it like that? Laziness, mostly. Hand computing the new CIGAR strings and what not seemed like a big pain when I could get the aligner to do it for me. All these issues could be resolved by moving to a reference free approach. That way one does not have to keep track of all this information and it's just created during a single final alignment. "}}