{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/5","labels_url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/5/comments","events_url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/5/events","html_url":"https://github.com/PacificBiosciences/PacBioFileFormats/issues/5","id":101541511,"number":5,"title":"need to add note to bam.pbi spec regarding CCS ","user":{"login":"dalexander","id":378620,"avatar_url":"https://avatars.githubusercontent.com/u/378620?v=3","gravatar_id":"","url":"https://api.github.com/users/dalexander","html_url":"https://github.com/dalexander","followers_url":"https://api.github.com/users/dalexander/followers","following_url":"https://api.github.com/users/dalexander/following{/other_user}","gists_url":"https://api.github.com/users/dalexander/gists{/gist_id}","starred_url":"https://api.github.com/users/dalexander/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dalexander/subscriptions","organizations_url":"https://api.github.com/users/dalexander/orgs","repos_url":"https://api.github.com/users/dalexander/repos","events_url":"https://api.github.com/users/dalexander/events{/privacy}","received_events_url":"https://api.github.com/users/dalexander/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-08-18T00:54:30Z","updated_at":"2015-08-18T22:42:15Z","closed_at":null,"body":"What is/should the bam.pbi look like for CCS input?  Current we populate qStart and qEnd with default values, corresponding to the absence of the qs, qe tags; this is good but Nat has pointed out that this means there's no way to see the read lengths from the bam.pbi file."},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/comments/132377750","html_url":"https://github.com/PacificBiosciences/PacBioFileFormats/issues/5#issuecomment-132377750","issue_url":"https://api.github.com/repos/PacificBiosciences/PacBioFileFormats/issues/5","id":132377750,"user":{"login":"natechols","id":4529952,"avatar_url":"https://avatars.githubusercontent.com/u/4529952?v=3","gravatar_id":"","url":"https://api.github.com/users/natechols","html_url":"https://github.com/natechols","followers_url":"https://api.github.com/users/natechols/followers","following_url":"https://api.github.com/users/natechols/following{/other_user}","gists_url":"https://api.github.com/users/natechols/gists{/gist_id}","starred_url":"https://api.github.com/users/natechols/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/natechols/subscriptions","organizations_url":"https://api.github.com/users/natechols/orgs","repos_url":"https://api.github.com/users/natechols/repos","events_url":"https://api.github.com/users/natechols/events{/privacy}","received_events_url":"https://api.github.com/users/natechols/received_events","type":"User","site_admin":false},"created_at":"2015-08-18T22:42:15Z","updated_at":"2015-08-18T22:42:15Z","body":"The files are small but iterating over many records in Python is still pretty slow, and it happens in many places.  I think there are some inefficiencies in our code that could be improved (I may have just figured out how to fix some of them), but even 20MB of CCS reads can take a while to get through.  My vote would be for adding readLength and np; I'm agnostic on the qs/qe semantics issue."}}