{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/471","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/471/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/471/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/471/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/471","id":186160636,"number":471,"title":"quick question:  does raw_reads daligner compare *all* reads against *all* reads or","user":{"login":"dgordon562","id":11529099,"avatar_url":"https://avatars.githubusercontent.com/u/11529099?v=3","gravatar_id":"","url":"https://api.github.com/users/dgordon562","html_url":"https://github.com/dgordon562","followers_url":"https://api.github.com/users/dgordon562/followers","following_url":"https://api.github.com/users/dgordon562/following{/other_user}","gists_url":"https://api.github.com/users/dgordon562/gists{/gist_id}","starred_url":"https://api.github.com/users/dgordon562/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dgordon562/subscriptions","organizations_url":"https://api.github.com/users/dgordon562/orgs","repos_url":"https://api.github.com/users/dgordon562/repos","events_url":"https://api.github.com/users/dgordon562/events{/privacy}","received_events_url":"https://api.github.com/users/dgordon562/received_events","type":"User","site_admin":false},"labels":[{"id":73826244,"url":"https://api.github.com/repos/PacificBiosciences/FALCON/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2016-10-30T20:25:23Z","updated_at":"2016-10-31T17:40:08Z","closed_at":"2016-10-30T22:26:50Z","body":"does it just compare _all_ reads against reads longer than length_cutoff?\n\nthanks!\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/257364305","html_url":"https://github.com/PacificBiosciences/FALCON/issues/471#issuecomment-257364305","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/471","id":257364305,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2016-10-31T17:40:08Z","updated_at":"2016-10-31T17:40:08Z","body":"@pb-jchin, Yes, in the output you are correct. But the algorithm actually compares *all* reads in the DB that are at least as long as the shortest *overlap*, which is the `-l` parameter. The algorithm ignores the `-H` parameter (our length-cutoff), which is only for final dumping of `.las` files.\r\n\r\n@dgordon562, I wasn't sure whether you are worried about total runtime/memory, or the final result. Sorry if I've caused confusion."}}
{"actor":{"display_login":"pb-cdunn"}}