GitHub PullRequestEvent at 2014-07-18 09:49:24
Repository: sickle
Actor: najoshi
Payload: {"action":"closed","number":27,"pull_request":{"url":"https://api.github.com/repos/najoshi/sickle/pulls/27","id":15707399,"html_url":"https://github.com/najoshi/sickle/pull/27","diff_url":"https://github.com/najoshi/sickle/pull/27.diff","patch_url":"https://github.com/najoshi/sickle/pull/27.patch","issue_url":"https://api.github.com/repos/najoshi/sickle/issues/27","number":27,"state":"closed","title":"Tuned sliding.c and added support for colorspace","user":{"login":"biocyberman","id":447942,"avatar_url":"https://avatars.githubusercontent.com/u/447942?","gravatar_id":"bd0b7d4ff3d230077c16f4ea9fc29747","url":"https://api.github.com/users/biocyberman","html_url":"https://github.com/biocyberman","followers_url":"https://api.github.com/users/biocyberman/followers","following_url":"https://api.github.com/users/biocyberman/following{/other_user}","gists_url":"https://api.github.com/users/biocyberman/gists{/gist_id}","starred_url":"https://api.github.com/users/biocyberman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocyberman/subscriptions","organizations_url":"https://api.github.com/users/biocyberman/orgs","repos_url":"https://api.github.com/users/biocyberman/repos","events_url":"https://api.github.com/users/biocyberman/events{/privacy}","received_events_url":"https://api.github.com/users/biocyberman/received_events","type":"User","site_admin":false},"body":"Hi, \r\nThanks for sharing `sickle`. \r\n\r\nI did some tuning of sliding.c in https://github.com/biocyberman/sickle/commit/efc18a4 commit, and added support for colorspace in  https://github.com/biocyberman/sickle/commit/cc02945 commit. The new sliding.c will first try to identify five_prime_cut and three_prime_cut and ignore -x flag at this stage. When the two cut point are found, then it start considering -x flag and reset five_prime_cut. I also made small adjustment on three_prime_cut initialization (to 'fqrec->qual.l - 1' instead of fqrec->seq.l).\r\n\r\nIn trim_single.c I added option to cope with base sequence prefix in color-space sequence. And when this option is used, `sickle` disables five_prime_cut when printing output.   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