{"action":"created","issue":{"url":"https://api.github.com/repos/mozack/abra/issues/13","labels_url":"https://api.github.com/repos/mozack/abra/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/mozack/abra/issues/13/comments","events_url":"https://api.github.com/repos/mozack/abra/issues/13/events","html_url":"https://github.com/mozack/abra/issues/13","id":53897745,"number":13,"title":"does abra realign unaligned reads ","user":{"login":"dwaggott","id":3149944,"avatar_url":"https://avatars.githubusercontent.com/u/3149944?v=3","gravatar_id":"","url":"https://api.github.com/users/dwaggott","html_url":"https://github.com/dwaggott","followers_url":"https://api.github.com/users/dwaggott/followers","following_url":"https://api.github.com/users/dwaggott/following{/other_user}","gists_url":"https://api.github.com/users/dwaggott/gists{/gist_id}","starred_url":"https://api.github.com/users/dwaggott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwaggott/subscriptions","organizations_url":"https://api.github.com/users/dwaggott/orgs","repos_url":"https://api.github.com/users/dwaggott/repos","events_url":"https://api.github.com/users/dwaggott/events{/privacy}","received_events_url":"https://api.github.com/users/dwaggott/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-01-09T18:17:58Z","updated_at":"2015-01-30T16:18:30Z","closed_at":null,"body":"Very cool project!\r\n\r\nDoes the code currently (a) try and salvage unaligned reads and (b) distant reads with potential alternate alignments. This would help for the events I'm looking for. i.e. long indels which initially don't align and variants in highly homologous ion channels.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/mozack/abra/issues/comments/72226137","html_url":"https://github.com/mozack/abra/issues/13#issuecomment-72226137","issue_url":"https://api.github.com/repos/mozack/abra/issues/13","id":72226137,"user":{"login":"mozack","id":1452590,"avatar_url":"https://avatars.githubusercontent.com/u/1452590?v=3","gravatar_id":"","url":"https://api.github.com/users/mozack","html_url":"https://github.com/mozack","followers_url":"https://api.github.com/users/mozack/followers","following_url":"https://api.github.com/users/mozack/following{/other_user}","gists_url":"https://api.github.com/users/mozack/gists{/gist_id}","starred_url":"https://api.github.com/users/mozack/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mozack/subscriptions","organizations_url":"https://api.github.com/users/mozack/orgs","repos_url":"https://api.github.com/users/mozack/repos","events_url":"https://api.github.com/users/mozack/events{/privacy}","received_events_url":"https://api.github.com/users/mozack/received_events","type":"User","site_admin":false},"created_at":"2015-01-30T16:18:30Z","updated_at":"2015-01-30T16:18:30Z","body":"Can you tell me a little more about the features you're looking for?  Do you have a sample dataset you could share?\r\n\r\nEarlier implementations assembled the unaligned reads together, mapped contigs to the reference, mapped reads to the contigs and assigned a provisional location to the reads for inclusion in the standard localized assembly.  Will need to do some digging to get a feel for what re-enabling this will take."}}