{"action":"created","issue":{"url":"https://api.github.com/repos/edawson/rkmh/issues/1","repository_url":"https://api.github.com/repos/edawson/rkmh","labels_url":"https://api.github.com/repos/edawson/rkmh/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/edawson/rkmh/issues/1/comments","events_url":"https://api.github.com/repos/edawson/rkmh/issues/1/events","html_url":"https://github.com/edawson/rkmh/issues/1","id":162914313,"number":1,"title":"Threading is bad","user":{"login":"edawson","id":2595153,"avatar_url":"https://avatars.githubusercontent.com/u/2595153?v=3","gravatar_id":"","url":"https://api.github.com/users/edawson","html_url":"https://github.com/edawson","followers_url":"https://api.github.com/users/edawson/followers","following_url":"https://api.github.com/users/edawson/following{/other_user}","gists_url":"https://api.github.com/users/edawson/gists{/gist_id}","starred_url":"https://api.github.com/users/edawson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edawson/subscriptions","organizations_url":"https://api.github.com/users/edawson/orgs","repos_url":"https://api.github.com/users/edawson/repos","events_url":"https://api.github.com/users/edawson/events{/privacy}","received_events_url":"https://api.github.com/users/edawson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/edawson/rkmh/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-06-29T12:37:01Z","updated_at":"2016-07-06T20:49:52Z","closed_at":null,"body":"Threads seem to be spending a lot of time waiting/instantiating, rather than doing real work. This is probably just a matter of moving around the OpenMP calls and moving from a map<string, hashes> to a vector<pair<string, hashes> > to allow parallel comparison of reads and refs."},"comment":{"url":"https://api.github.com/repos/edawson/rkmh/issues/comments/230901980","html_url":"https://github.com/edawson/rkmh/issues/1#issuecomment-230901980","issue_url":"https://api.github.com/repos/edawson/rkmh/issues/1","id":230901980,"user":{"login":"edawson","id":2595153,"avatar_url":"https://avatars.githubusercontent.com/u/2595153?v=3","gravatar_id":"","url":"https://api.github.com/users/edawson","html_url":"https://github.com/edawson","followers_url":"https://api.github.com/users/edawson/followers","following_url":"https://api.github.com/users/edawson/following{/other_user}","gists_url":"https://api.github.com/users/edawson/gists{/gist_id}","starred_url":"https://api.github.com/users/edawson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edawson/subscriptions","organizations_url":"https://api.github.com/users/edawson/orgs","repos_url":"https://api.github.com/users/edawson/repos","events_url":"https://api.github.com/users/edawson/events{/privacy}","received_events_url":"https://api.github.com/users/edawson/received_events","type":"User","site_admin":false},"created_at":"2016-07-06T20:49:52Z","updated_at":"2016-07-06T20:49:52Z","body":"I use 'std::string::substr' to make the kmers and pass the newly-generated vector of strings to the hash function. I should probably just take slices of the char* pointing to the input sequence, which will save like 7000 string instantiations per read. "}}
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