{"action":"opened","issue":{"url":"https://api.github.com/repos/rrwick/Bandage/issues/21","repository_url":"https://api.github.com/repos/rrwick/Bandage","labels_url":"https://api.github.com/repos/rrwick/Bandage/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/rrwick/Bandage/issues/21/comments","events_url":"https://api.github.com/repos/rrwick/Bandage/issues/21/events","html_url":"https://github.com/rrwick/Bandage/issues/21","id":151166502,"number":21,"title":"Read Coverage vs. Read Count, when nodes exporting to .gfa from LastgGraph.","user":{"login":"Omig12","id":6131141,"avatar_url":"https://avatars.githubusercontent.com/u/6131141?v=3","gravatar_id":"","url":"https://api.github.com/users/Omig12","html_url":"https://github.com/Omig12","followers_url":"https://api.github.com/users/Omig12/followers","following_url":"https://api.github.com/users/Omig12/following{/other_user}","gists_url":"https://api.github.com/users/Omig12/gists{/gist_id}","starred_url":"https://api.github.com/users/Omig12/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Omig12/subscriptions","organizations_url":"https://api.github.com/users/Omig12/orgs","repos_url":"https://api.github.com/users/Omig12/repos","events_url":"https://api.github.com/users/Omig12/events{/privacy}","received_events_url":"https://api.github.com/users/Omig12/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-26T15:31:39Z","updated_at":"2016-04-26T15:31:39Z","closed_at":null,"body":"Hi Ryan, \r\n\r\nFirst of all many I'd like to thanks you for this awesome tool. Now to the issue, while working on a LastGraph to GFA parser, when utilizing Bandage 7.1 to corroborate the specification of the connected components reported by the parser, we noticed that when exporting selected nodes from LastGraph file to GFA, the output file generated by Bandage reports appears to be an incorrect value in the GFA sequence's read count optional header.\r\n\r\nFrom what I could gather the GFA sequence's read count _(RC:i:###)_ is being retrieved using LastGraph's _$COV_SHORT1_ value from the NODE header, instead of the _$NUMBER_OF_SHORT_READS_ value from the NR header.\r\n\r\n**[LastGraph](http://computing.bio.cam.ac.uk/local/doc/velvet.pdf)**\r\n`NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT2 $O_COV_SHORT2`\r\n\r\n`NR $NODE_ID $NUMBER_OF_SHORT_READS`\r\n\r\n**[GFA](https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md)** \r\n`S    RC    i    # reads assembled into the segment`\r\n\r\n`L/S  RC    i    # reads that support the segment/link`\r\n\r\nI'm an undergrad student currently working on my first semester of Bioinformatics research, so I might be mistaking the terms used in the documentation for the file formats.  Anyways, I hope this is a useful contribution. "}}