{"action":"created","issue":{"url":"https://api.github.com/repos/etal/cnvkit/issues/87","repository_url":"https://api.github.com/repos/etal/cnvkit","labels_url":"https://api.github.com/repos/etal/cnvkit/issues/87/labels{/name}","comments_url":"https://api.github.com/repos/etal/cnvkit/issues/87/comments","events_url":"https://api.github.com/repos/etal/cnvkit/issues/87/events","html_url":"https://github.com/etal/cnvkit/issues/87","id":141287801,"number":87,"title":"Running individual commands instead of 'batch' does not yield same *.cns file","user":{"login":"nriMH","id":17880747,"avatar_url":"https://avatars.githubusercontent.com/u/17880747?v=3","gravatar_id":"","url":"https://api.github.com/users/nriMH","html_url":"https://github.com/nriMH","followers_url":"https://api.github.com/users/nriMH/followers","following_url":"https://api.github.com/users/nriMH/following{/other_user}","gists_url":"https://api.github.com/users/nriMH/gists{/gist_id}","starred_url":"https://api.github.com/users/nriMH/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nriMH/subscriptions","organizations_url":"https://api.github.com/users/nriMH/orgs","repos_url":"https://api.github.com/users/nriMH/repos","events_url":"https://api.github.com/users/nriMH/events{/privacy}","received_events_url":"https://api.github.com/users/nriMH/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/etal/cnvkit/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-03-16T14:13:56Z","updated_at":"2016-03-30T18:02:50Z","closed_at":null,"body":"Hi,\r\n\r\nI am doing some parameter optimization with CNVkit (v0.7.5), which is why I replaced the 'batch' command by the individual commands as described in the documentation:\r\n\r\n- target\r\n- antitarget\r\n- coverage\r\n- reference\r\n- fix\r\n- segment\r\n\r\nWhen running these with default parameters, they generate the same files as the batch command does, until the *.cnr file generated by the 'fix' command. The *cnr files are almost the same, except for the log2 values which are very similar, as for example:\r\n\r\n< chr1\t1146873\t1147108\tTNFRSF4\t-0.84963\t0.588972\r\n< chr1\t1147108\t1147343\tTNFRSF4\t-0.74046\t0.588972\r\n< chr1\t1147343\t1147578\tTNFRSF4\t-0.97845\t0.588972\r\n< chr1\t1147982\t1148222\tTNFRSF4\t-1.20474\t0.601504\r\n< chr1\t1148302\t1148542\tTNFRSF4\t-1.24132\t0.601504\r\n< chr1\t1148706\t1148946\tTNFRSF4\t-1.21758\t0.601504\r\n< chr1\t1148983\t1149223\tTNFRSF4\t-1.19841\t0.601504\r\n< chr1\t1149294\t1149574\tTNFRSF4\t-1.06558\t0.701754\r\n---\r\n> chr1\t1146873\t1147108\tTNFRSF4\t-0.851124\t0.588972\r\n> chr1\t1147108\t1147343\tTNFRSF4\t-0.822549\t0.588972\r\n> chr1\t1147343\t1147578\tTNFRSF4\t-0.984025\t0.588972\r\n> chr1\t1147982\t1148222\tTNFRSF4\t-1.19129\t0.601504\r\n> chr1\t1148302\t1148542\tTNFRSF4\t-1.24459\t0.601504\r\n> chr1\t1148706\t1148946\tTNFRSF4\t-1.21221\t0.601504\r\n> chr1\t1148983\t1149223\tTNFRSF4\t-1.19624\t0.601504\r\n> chr1\t1149294\t1149574\tTNFRSF4\t-1.06491\t0.701754\r\n\r\nThe major issue, though, is that based on this very similar *.cnr file, the 'segment' command (cnvkit.py segment myfile.cnr -o myfile.cns) yields a totally different amount of regions (compared to the batch command) in the resulting *.cns file! Am I missing a default parameter? I tried adding some (like --drop-outliers) but to no avail.\r\n\r\nThanks a lot!"},"comment":{"url":"https://api.github.com/repos/etal/cnvkit/issues/comments/203555968","html_url":"https://github.com/etal/cnvkit/issues/87#issuecomment-203555968","issue_url":"https://api.github.com/repos/etal/cnvkit/issues/87","id":203555968,"user":{"login":"etal","id":52723,"avatar_url":"https://avatars.githubusercontent.com/u/52723?v=3","gravatar_id":"","url":"https://api.github.com/users/etal","html_url":"https://github.com/etal","followers_url":"https://api.github.com/users/etal/followers","following_url":"https://api.github.com/users/etal/following{/other_user}","gists_url":"https://api.github.com/users/etal/gists{/gist_id}","starred_url":"https://api.github.com/users/etal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/etal/subscriptions","organizations_url":"https://api.github.com/users/etal/orgs","repos_url":"https://api.github.com/users/etal/repos","events_url":"https://api.github.com/users/etal/events{/privacy}","received_events_url":"https://api.github.com/users/etal/received_events","type":"User","site_admin":false},"created_at":"2016-03-30T18:02:50Z","updated_at":"2016-03-30T18:02:50Z","body":"I think there may be a difference in default settings between `batch` and either `fix` or `reference`. I'll see if I can find it; sorry for the trouble and delay."}}