{"action":"created","issue":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/233","repository_url":"https://api.github.com/repos/fulcrumgenomics/fgbio","labels_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/233/labels{/name}","comments_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/233/comments","events_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/233/events","html_url":"https://github.com/fulcrumgenomics/fgbio/pull/233","id":229557086,"number":233,"title":"Clip a fixed amount on the 5' end of reads.","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars2.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":"nh13","id":846274,"avatar_url":"https://avatars2.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},"assignees":[{"login":"nh13","id":846274,"avatar_url":"https://avatars2.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}],"milestone":null,"comments":1,"created_at":"2017-05-18T05:13:23Z","updated_at":"2017-05-19T21:24:02Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/233","html_url":"https://github.com/fulcrumgenomics/fgbio/pull/233","diff_url":"https://github.com/fulcrumgenomics/fgbio/pull/233.diff","patch_url":"https://github.com/fulcrumgenomics/fgbio/pull/233.patch"},"body":"\r\n@tfenne I was loathe to create yet-another-tool and chain these together because:\r\n1. I would have to add a output `sort order` to one of the two tools so that we don't sort unnecessarily (`coordinate -> query -> coordinate` twice).\r\n2. The actual amount of code is so little, I would hate to duplicate it.\r\nThe option I _could_ do is to create another tool called `ClipReads` and have `ClipOverlappingReads` extend it but fix `numStartClip=0`.  That way we have the previous tool and a new tool, though the documentation (usage and arg annotations) would be duplicated.  Therefore I chose not to go down this route. "},"comment":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/comments/302814590","html_url":"https://github.com/fulcrumgenomics/fgbio/pull/233#issuecomment-302814590","issue_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/233","id":302814590,"user":{"login":"nh13","id":846274,"avatar_url":"https://avatars2.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":"2017-05-19T21:24:02Z","updated_at":"2017-05-19T21:24:02Z","body":"Added a few more tests and created the `ClipBam` tool.  Rebased onto master (not _that_ bad).  I am merging when tests pass."}}
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