{"action":"created","issue":{"url":"https://api.github.com/repos/ged-lab/khmer/issues/745","labels_url":"https://api.github.com/repos/ged-lab/khmer/issues/745/labels{/name}","comments_url":"https://api.github.com/repos/ged-lab/khmer/issues/745/comments","events_url":"https://api.github.com/repos/ged-lab/khmer/issues/745/events","html_url":"https://github.com/ged-lab/khmer/issues/745","id":55808650,"number":745,"title":"normalize-by-median.py --force default should be 'true'","user":{"login":"macmanes","id":164752,"avatar_url":"https://avatars.githubusercontent.com/u/164752?v=3","gravatar_id":"","url":"https://api.github.com/users/macmanes","html_url":"https://github.com/macmanes","followers_url":"https://api.github.com/users/macmanes/followers","following_url":"https://api.github.com/users/macmanes/following{/other_user}","gists_url":"https://api.github.com/users/macmanes/gists{/gist_id}","starred_url":"https://api.github.com/users/macmanes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macmanes/subscriptions","organizations_url":"https://api.github.com/users/macmanes/orgs","repos_url":"https://api.github.com/users/macmanes/repos","events_url":"https://api.github.com/users/macmanes/events{/privacy}","received_events_url":"https://api.github.com/users/macmanes/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ged-lab/khmer/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/ged-lab/khmer/labels/low-hanging-fruit","name":"low-hanging-fruit","color":"eb6420"},{"url":"https://api.github.com/repos/ged-lab/khmer/labels/Python","name":"Python","color":"5319e7"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/ged-lab/khmer/milestones/12","labels_url":"https://api.github.com/repos/ged-lab/khmer/milestones/12/labels","id":739801,"number":12,"title":"1.3+","description":"","creator":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"open_issues":63,"closed_issues":14,"state":"open","created_at":"2014-08-01T14:28:22Z","updated_at":"2015-02-23T04:13:30Z","due_on":null,"closed_at":null},"comments":6,"created_at":"2015-01-28T20:11:08Z","updated_at":"2015-02-23T04:31:56Z","closed_at":null,"body":"In messing around with `normalize-by-median.py`, I realized that if I killed a run while it was running, then issued a new command using the same output filename, that the product of the new command was *appended* to the results of the first command. __I don't think this is ever when the user wants__ - a set of reads will be duplicated in the normalized output file.. I think that the output should always be overwritten `--force TRUE` with or without a warning that the file is being overwritten.. \r\n\r\n    grep HWI-ST1097:199:D22V1ACXX:1:1101:1154:2129 khmer.normalized.C50.fastq\r\n    >HWI-ST1097:199:D22V1ACXX:1:1101:1154:2129/1\r\n    >HWI-ST1097:199:D22V1ACXX:1:1101:1154:2129/2\r\n    >HWI-ST1097:199:D22V1ACXX:1:1101:1154:2129/1\r\n    >HWI-ST1097:199:D22V1ACXX:1:1101:1154:2129/2\r\n\r\n\r\nMy 2cents "},"comment":{"url":"https://api.github.com/repos/ged-lab/khmer/issues/comments/75488346","html_url":"https://github.com/ged-lab/khmer/issues/745#issuecomment-75488346","issue_url":"https://api.github.com/repos/ged-lab/khmer/issues/745","id":75488346,"user":{"login":"drtamermansour","id":6537740,"avatar_url":"https://avatars.githubusercontent.com/u/6537740?v=3","gravatar_id":"","url":"https://api.github.com/users/drtamermansour","html_url":"https://github.com/drtamermansour","followers_url":"https://api.github.com/users/drtamermansour/followers","following_url":"https://api.github.com/users/drtamermansour/following{/other_user}","gists_url":"https://api.github.com/users/drtamermansour/gists{/gist_id}","starred_url":"https://api.github.com/users/drtamermansour/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drtamermansour/subscriptions","organizations_url":"https://api.github.com/users/drtamermansour/orgs","repos_url":"https://api.github.com/users/drtamermansour/repos","events_url":"https://api.github.com/users/drtamermansour/events{/privacy}","received_events_url":"https://api.github.com/users/drtamermansour/received_events","type":"User","site_admin":false},"created_at":"2015-02-23T04:31:56Z","updated_at":"2015-02-23T04:31:56Z","body":"This function does not make sense for me:\r\nhttps://github.com/ged-lab/khmer/blob/master/scripts/normalize-by-median.py#L221\r\nI tracked the implementation of the function here\r\nhttps://github.com/drtamermansour/khmer/blob/fix/%23745/khmer/kfile.py#L43\r\nIt uses the size of the input files to make a decision about the available desk space !!! \r\n"}}