{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/1435","repository_url":"https://api.github.com/repos/dib-lab/khmer","labels_url":"https://api.github.com/repos/dib-lab/khmer/issues/1435/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/khmer/issues/1435/comments","events_url":"https://api.github.com/repos/dib-lab/khmer/issues/1435/events","html_url":"https://github.com/dib-lab/khmer/pull/1435","id":174904346,"number":1435,"title":"fix lowercase actgn input handling.","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-09-03T16:27:52Z","updated_at":"2016-10-03T20:20:17Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/dib-lab/khmer/pulls/1435","html_url":"https://github.com/dib-lab/khmer/pull/1435","diff_url":"https://github.com/dib-lab/khmer/pull/1435.diff","patch_url":"https://github.com/dib-lab/khmer/pull/1435.patch"},"body":"This is a fix for #1434.\r\n\r\nAdds a 'cleaned_seq' attribute to screed records that should be used whenever k-mer operations are performed, and propagates this attribute through the codebase with associated refactorings of ReadBundle, trim-low-abund, and normalize-by-median.\r\n\r\nThe key bugfix commit is 7b40857, which makes the key change to normalize-by-median to uppercase sequences before adding them to the graph.  Prior to this, all k-mers containing lower-case characters would simply be ignored.  Note that this changes output formats, so the md5 hashes in test_script_output.py have been updated.  Since this is a bug and not a new feature, I think semantic versioning will permit a 2.x release.  Also note that the output of trim-low-abund.py matches the output of normalize-by-median.py despite quite different implementations, suggesting that both are correct :).\r\n\r\n- [x] Is it mergeable?\r\n- [x] `make test` Did it pass the tests?\r\n- [x] `make clean diff-cover` If it introduces new functionality in\r\n  `scripts/` is it tested?\r\n- [x] `make format diff_pylint_report cppcheck doc pydocstyle` Is it well\r\n  formatted?\r\n- [x] Did it change the command-line interface? Only additions are allowed\r\n  without a major version increment. Changing file formats also requires a\r\n  major version number increment.\r\n- [x] Is it documented in the `ChangeLog`?\r\n  http://en.wikipedia.org/wiki/Changelog#Format\r\n- [x] Was a spellchecker run on the source code and documentation after\r\n  changes were made?\r\n- [x] Do the changes respect streaming IO? (Are they\r\n  tested for streaming IO?)\r\n- [x] Is the Copyright year up to date?\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/comments/251214967","html_url":"https://github.com/dib-lab/khmer/pull/1435#issuecomment-251214967","issue_url":"https://api.github.com/repos/dib-lab/khmer/issues/1435","id":251214967,"user":{"login":"standage","id":566823,"avatar_url":"https://avatars.githubusercontent.com/u/566823?v=3","gravatar_id":"","url":"https://api.github.com/users/standage","html_url":"https://github.com/standage","followers_url":"https://api.github.com/users/standage/followers","following_url":"https://api.github.com/users/standage/following{/other_user}","gists_url":"https://api.github.com/users/standage/gists{/gist_id}","starred_url":"https://api.github.com/users/standage/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/standage/subscriptions","organizations_url":"https://api.github.com/users/standage/orgs","repos_url":"https://api.github.com/users/standage/repos","events_url":"https://api.github.com/users/standage/events{/privacy}","received_events_url":"https://api.github.com/users/standage/received_events","type":"User","site_admin":false},"created_at":"2016-10-03T20:20:17Z","updated_at":"2016-10-03T20:20:17Z","body":"Yep al teh wrods is gud,"}}
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