{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/653","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/653/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/653/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/653/events","html_url":"https://github.com/bigdatagenomics/adam/pull/653","id":69390046,"number":653,"title":"ADAM issue #410","user":{"login":"bryanjj","id":3630871,"avatar_url":"https://avatars.githubusercontent.com/u/3630871?v=3","gravatar_id":"","url":"https://api.github.com/users/bryanjj","html_url":"https://github.com/bryanjj","followers_url":"https://api.github.com/users/bryanjj/followers","following_url":"https://api.github.com/users/bryanjj/following{/other_user}","gists_url":"https://api.github.com/users/bryanjj/gists{/gist_id}","starred_url":"https://api.github.com/users/bryanjj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bryanjj/subscriptions","organizations_url":"https://api.github.com/users/bryanjj/orgs","repos_url":"https://api.github.com/users/bryanjj/repos","events_url":"https://api.github.com/users/bryanjj/events{/privacy}","received_events_url":"https://api.github.com/users/bryanjj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-04-19T05:58:18Z","updated_at":"2015-04-19T06:52:48Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/653","html_url":"https://github.com/bigdatagenomics/adam/pull/653","diff_url":"https://github.com/bigdatagenomics/adam/pull/653.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/653.patch"},"body":"I was interested in contributing to this project and learning scala.\r\nI am attempting to partially address https://github.com/bigdatagenomics/adam/issues/410\r\n\r\nI created a new alphabet class which operates on symbols.  I based the functionality on the existing SequenceUtils class which supports the following functionality:\r\n1. basic DNA symbols\r\n2. case-insensitivity\r\n3. reverse complement function which leaves unknown chars unchanged\r\n\r\nMy main concerns with this pull request are\r\n1. I'm just learning scala so might be doing something dumb\r\n2. I'm not sure which package this class should go in\r\n3. I think performance should be ok because the String map function uses a StringBuilder internally, but not sure about overhead on case class creation or exception handling for unknown characters\r\n4. This issue also mentions \"ambiguity codes\", but I'm not sure what they are but should be able to add later if they're needed\r\n\r\nthis is my first github contribution ever so let me know what you think"},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/94245257","html_url":"https://github.com/bigdatagenomics/adam/pull/653#issuecomment-94245257","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/653","id":94245257,"user":{"login":"AmplabJenkins","id":4031291,"avatar_url":"https://avatars.githubusercontent.com/u/4031291?v=3","gravatar_id":"","url":"https://api.github.com/users/AmplabJenkins","html_url":"https://github.com/AmplabJenkins","followers_url":"https://api.github.com/users/AmplabJenkins/followers","following_url":"https://api.github.com/users/AmplabJenkins/following{/other_user}","gists_url":"https://api.github.com/users/AmplabJenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/AmplabJenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AmplabJenkins/subscriptions","organizations_url":"https://api.github.com/users/AmplabJenkins/orgs","repos_url":"https://api.github.com/users/AmplabJenkins/repos","events_url":"https://api.github.com/users/AmplabJenkins/events{/privacy}","received_events_url":"https://api.github.com/users/AmplabJenkins/received_events","type":"User","site_admin":false},"created_at":"2015-04-19T06:52:48Z","updated_at":"2015-04-19T06:52:48Z","body":"Test PASSed.\nRefer to this link for build results (access rights to CI server needed): \nhttps://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/677/\nTest PASSed."}}