{"action":"opened","issue":{"url":"https://api.github.com/repos/VDBWRAIR/Haskell-MAAPs/issues/2","repository_url":"https://api.github.com/repos/VDBWRAIR/Haskell-MAAPs","labels_url":"https://api.github.com/repos/VDBWRAIR/Haskell-MAAPs/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/VDBWRAIR/Haskell-MAAPs/issues/2/comments","events_url":"https://api.github.com/repos/VDBWRAIR/Haskell-MAAPs/issues/2/events","html_url":"https://github.com/VDBWRAIR/Haskell-MAAPs/issues/2","id":158923759,"number":2,"title":"Feature Request: Add synonymous for completeness","user":{"login":"mmelendrez","id":2855130,"avatar_url":"https://avatars.githubusercontent.com/u/2855130?v=3","gravatar_id":"","url":"https://api.github.com/users/mmelendrez","html_url":"https://github.com/mmelendrez","followers_url":"https://api.github.com/users/mmelendrez/followers","following_url":"https://api.github.com/users/mmelendrez/following{/other_user}","gists_url":"https://api.github.com/users/mmelendrez/gists{/gist_id}","starred_url":"https://api.github.com/users/mmelendrez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmelendrez/subscriptions","organizations_url":"https://api.github.com/users/mmelendrez/orgs","repos_url":"https://api.github.com/users/mmelendrez/repos","events_url":"https://api.github.com/users/mmelendrez/events{/privacy}","received_events_url":"https://api.github.com/users/mmelendrez/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-06-07T13:32:02Z","updated_at":"2016-06-07T13:32:02Z","closed_at":null,"body":"To get a full idea of the ambiguity content within a sequence it's more accurate to also include those ambiguities that do not result in an amino acid change and label them as synonymous, otherwise when investigators compare the output to manually curated output I envision it will be initially confusing.\r\n\r\nRather than make it a native function perhaps just adding an option for the investigator to record all ambiguities. So the default can be mixed amino acid positions only but if the investigator wants synonymous too perhaps they can add the flag '--syn true' or just --syn"}}
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