{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1981","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1981/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1981/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1981/events","html_url":"https://github.com/broadinstitute/gatk/pull/1981","id":164346692,"number":1981,"title":"add bwa to reads pipeline","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"assignees":[{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false}],"milestone":null,"comments":7,"created_at":"2016-07-07T16:02:40Z","updated_at":"2016-08-02T17:17:28Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1981","html_url":"https://github.com/broadinstitute/gatk/pull/1981","diff_url":"https://github.com/broadinstitute/gatk/pull/1981.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1981.patch"},"body":"fixes https://github.com/broadinstitute/gatk/issues/1904\r\n\r\n2 hacks needed to be done for now:\r\n1) bwa loses tags so we keep track of which original read corresponds to which aligned read by creating a subclass of `ShortRead` (the class that jBWA uses for JNI) and putting the original read in a pointer in there.\r\n2) bwa requires a fasta reference while reads pipeline wants a 2bit reference (in the BROADCAST mode, which is the default). The workaround for now is to pass two reference files one of each kind"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/236975232","html_url":"https://github.com/broadinstitute/gatk/pull/1981#issuecomment-236975232","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1981","id":236975232,"user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"created_at":"2016-08-02T17:17:28Z","updated_at":"2016-08-02T17:17:28Z","body":"@droazen What's the plan for these dangling adam branches?  I'll do the review and make the changes myself?  "}}
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