{"action":"created","comment":{"url":"https://api.github.com/repos/dib-lab/khmer/pulls/comments/36360697","id":36360697,"diff_hunk":"@@ -110,6 +272,16 @@ def __call__(self, parser, namespace, values, option_string=None):\n ** Your values for ksize, n_tables, and tablesize\n ** will be ignored.'''.format(hashfile=values))\n \n+            if getattr(namespace, 'unique_kmers') != 0 or \\","path":"khmer/khmer_args.py","position":216,"original_position":216,"commit_id":"c523ef296377730f6a828dc04c3b3c7037c9b74e","original_commit_id":"c523ef296377730f6a828dc04c3b3c7037c9b74e","user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"body":"is there a reason not to use 'namespace.unique_kmers' and 'namespace.max_memory_usage' here?\r\n","created_at":"2015-08-05T22:08:39Z","updated_at":"2015-08-05T22:08:39Z","html_url":"https://github.com/dib-lab/khmer/pull/1214#discussion_r36360697","pull_request_url":"https://api.github.com/repos/dib-lab/khmer/pulls/1214","_links":{"self":{"href":"https://api.github.com/repos/dib-lab/khmer/pulls/comments/36360697"},"html":{"href":"https://github.com/dib-lab/khmer/pull/1214#discussion_r36360697"},"pull_request":{"href":"https://api.github.com/repos/dib-lab/khmer/pulls/1214"}}},"pull_request":{"url":"https://api.github.com/repos/dib-lab/khmer/pulls/1214","id":41286531,"html_url":"https://github.com/dib-lab/khmer/pull/1214","diff_url":"https://github.com/dib-lab/khmer/pull/1214.diff","patch_url":"https://github.com/dib-lab/khmer/pull/1214.patch","issue_url":"https://api.github.com/repos/dib-lab/khmer/issues/1214","number":1214,"state":"open","locked":false,"title":"Cleaning up automatic argument setting","user":{"login":"bocajnotnef","id":2142082,"avatar_url":"https://avatars.githubusercontent.com/u/2142082?v=3","gravatar_id":"","url":"https://api.github.com/users/bocajnotnef","html_url":"https://github.com/bocajnotnef","followers_url":"https://api.github.com/users/bocajnotnef/followers","following_url":"https://api.github.com/users/bocajnotnef/following{/other_user}","gists_url":"https://api.github.com/users/bocajnotnef/gists{/gist_id}","starred_url":"https://api.github.com/users/bocajnotnef/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bocajnotnef/subscriptions","organizations_url":"https://api.github.com/users/bocajnotnef/orgs","repos_url":"https://api.github.com/users/bocajnotnef/repos","events_url":"https://api.github.com/users/bocajnotnef/events{/privacy}","received_events_url":"https://api.github.com/users/bocajnotnef/received_events","type":"User","site_admin":false},"body":"Ref #1117 for expansion of automatic memory usage determination, this time based on estimated number of unique k-mers. Inspired by user experience upgrade goals (#732) and hopefully will fix #1179 (dealing with `-U/--unique-kmers`).\r\n\r\nThis resolves @ctb's comment https://github.com/dib-lab/khmer/issues/1117#issuecomment-126351063:\r\n\r\n>OK, well, let's start a new pull request :). Here are a few requested changes:\r\n\r\n> - change do_sanity_checking name to check_fp_rate\r\n> - should this function only be called if -U is set? For now, I think so...\r\n> - change oxutils shortname to oxfuncs, since it's `oxli.functions' you're importing.\r\n> - get rid of \"optimization\" language in comments - it's automatic argument picking, not optimization :)\r\n> (The goal of all of this is to enable script readability.)\r\n\r\n> Is there a reason that this code isn't called generically in create_countgraph/other khmer_args functions? 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