{"action":"created","issue":{"url":"https://api.github.com/repos/barricklab/breseq/issues/164","repository_url":"https://api.github.com/repos/barricklab/breseq","labels_url":"https://api.github.com/repos/barricklab/breseq/issues/164/labels{/name}","comments_url":"https://api.github.com/repos/barricklab/breseq/issues/164/comments","events_url":"https://api.github.com/repos/barricklab/breseq/issues/164/events","html_url":"https://github.com/barricklab/breseq/issues/164","id":329222945,"node_id":"MDU6SXNzdWUzMjkyMjI5NDU=","number":164,"title":"gdtools set operation bug","user":{"login":"vr1087","id":7674836,"node_id":"MDQ6VXNlcjc2NzQ4MzY=","avatar_url":"https://avatars1.githubusercontent.com/u/7674836?v=4","gravatar_id":"","url":"https://api.github.com/users/vr1087","html_url":"https://github.com/vr1087","followers_url":"https://api.github.com/users/vr1087/followers","following_url":"https://api.github.com/users/vr1087/following{/other_user}","gists_url":"https://api.github.com/users/vr1087/gists{/gist_id}","starred_url":"https://api.github.com/users/vr1087/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vr1087/subscriptions","organizations_url":"https://api.github.com/users/vr1087/orgs","repos_url":"https://api.github.com/users/vr1087/repos","events_url":"https://api.github.com/users/vr1087/events{/privacy}","received_events_url":"https://api.github.com/users/vr1087/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-04T21:25:33Z","updated_at":"2018-06-05T15:54:28Z","closed_at":null,"author_association":"NONE","body":"I am trying to use the gdtools 'subtract' function, but it is failing to correctly equate some mutations.\r\n\r\nI ran this command:\r\n`gdtools SUBTRACT -o subtract_failure.gd positives.gd predicted.gd`\r\n\r\nBut I still see mutations in 'subtract_failure.gd' that are in both input gd files. I've attached the genome Diff files. I can provide all the data if needed, however. \r\n\r\nI am using breseq 0.32.1 and \r\n`---> bowtie2  :: version 2.3.2 [/usr/local/bin/bowtie2] `\r\n`---> R        :: version 3.2.3 [/usr/bin/R]`\r\n\r\n[gd_files.zip](https://github.com/barricklab/breseq/files/2070011/gd_files.zip)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/barricklab/breseq/issues/comments/394763107","html_url":"https://github.com/barricklab/breseq/issues/164#issuecomment-394763107","issue_url":"https://api.github.com/repos/barricklab/breseq/issues/164","id":394763107,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDc2MzEwNw==","user":{"login":"jeffreybarrick","id":6777876,"node_id":"MDQ6VXNlcjY3Nzc4NzY=","avatar_url":"https://avatars2.githubusercontent.com/u/6777876?v=4","gravatar_id":"","url":"https://api.github.com/users/jeffreybarrick","html_url":"https://github.com/jeffreybarrick","followers_url":"https://api.github.com/users/jeffreybarrick/followers","following_url":"https://api.github.com/users/jeffreybarrick/following{/other_user}","gists_url":"https://api.github.com/users/jeffreybarrick/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffreybarrick/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffreybarrick/subscriptions","organizations_url":"https://api.github.com/users/jeffreybarrick/orgs","repos_url":"https://api.github.com/users/jeffreybarrick/repos","events_url":"https://api.github.com/users/jeffreybarrick/events{/privacy}","received_events_url":"https://api.github.com/users/jeffreybarrick/received_events","type":"User","site_admin":false},"created_at":"2018-06-05T15:54:28Z","updated_at":"2018-06-05T15:54:28Z","author_association":"CONTRIBUTOR","body":"I think there are two issues here:\r\n(1) The default behavior of SUBTRACT is to take the frequency of a mutation in file1 and subtract the frequency in file 2 and then remove the mutation from the results if the resulting frequency is 0 or less.\r\n(2) There is a floating point error that makes subtracting 1 from 1 not give the expected result.\r\n\r\nI'd like to change the _default_ behavior to be removing the mutation in file1 if it is present with *any* frequency in file2 (essentially throwing out all frequency information in the input and output files). But, I think I'll add an option to preserve the frequency subtraction version with the floating point fix.\r\n\r\nDoes this make sense? Is that the default behavior you'd expect – only keeping track of entries not frequencies? Or would you expect it to pay attention to the frequencies of the mutations by default?"}}
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