{"action":"created","issue":{"url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/20","repository_url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc","labels_url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/20/comments","events_url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/20/events","html_url":"https://github.com/fulcrumgenomics/JeanLuc/pull/20","id":133621716,"number":20,"title":"Using dagr-sopt for command line parsing and starting the move to scala","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2016-02-15T04:40:56Z","updated_at":"2016-02-18T21:07:10Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/pulls/20","html_url":"https://github.com/fulcrumgenomics/JeanLuc/pull/20","diff_url":"https://github.com/fulcrumgenomics/JeanLuc/pull/20.diff","patch_url":"https://github.com/fulcrumgenomics/JeanLuc/pull/20.patch"},"body":"This PR demonstrates:\r\n- using `dagr-sopt` for command line parsing (see https://github.com/fulcrumgenomics/dagr/pull/83)\r\n- `FilterBam` is now pure scala; I deleted the other tools in the second commit for this demonstration.\r\n- build with `sbt`\r\n\r\nRequirements:\r\n- `sbt publishLocal` using the dagr branch here: https://github.com/fulcrumgenomics/dagr/pull/83\r\n- `sbt assembly` to build the jeanluc jar\r\n\r\nTo be done:\r\n- convert the rest of the tools to scala\r\n- update `.travis.yml` among other things\r\n\r\nThoughts:\r\n- the various tools *could* be run in `dagr` if wrapped in `SimpleInJvmTasks` :)"},"comment":{"url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/comments/185921535","html_url":"https://github.com/fulcrumgenomics/JeanLuc/pull/20#issuecomment-185921535","issue_url":"https://api.github.com/repos/fulcrumgenomics/JeanLuc/issues/20","id":185921535,"user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"created_at":"2016-02-18T21:07:10Z","updated_at":"2016-02-18T21:07:10Z","body":"I propose we create PRs to this PR for each tool:\r\n- [ ] `main/java/com/fulcrumgenomics/bam/FilterBam.java`\r\n- [ ] `main/java/com/fulcrumgenomics/cmdline/Main.java`\r\n- [ ] `main/java/com/fulcrumgenomics/cmdline/Personal.java`\r\n- [ ] `main/java/com/fulcrumgenomics/cmdline/Utilities.java`\r\n- [ ] `main/java/com/fulcrumgenomics/metrics/CalculateQualityScoreAccuracy.java`\r\n- [ ] `main/java/com/fulcrumgenomics/metrics/CollectWgsMetricsWithHistogram.java`\r\n- [ ] `main/java/com/fulcrumgenomics/personal/nhomer/GenerateRegionsFromFasta.java`\r\n- [ ] `main/java/com/fulcrumgenomics/personal/nhomer/HasSequence.java`\r\n- [ ] `main/java/com/fulcrumgenomics/personal/nhomer/SplitTag.java`\r\n- [ ] `main/java/com/fulcrumgenomics/personal/tfenne/MakeGermlineMixtureVcf.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/AnnotateVcfWithCoverageStats.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/DemuxFastqs.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/DnaFoldPrediction.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/DnaFoldPredictor.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/PickIlluminaIndices.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/SequentialFastqReader.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/miseq/Sample.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/miseq/SampleBarcode.java`\r\n- [ ] `main/java/com/fulcrumgenomics/util/miseq/SampleSheet.java`\r\n"}}