{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1277","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1277/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1277/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1277/events","html_url":"https://github.com/bigdatagenomics/adam/pull/1277","id":190118694,"number":1277,"title":"use ParsedLoci in loadIndexedBam","user":{"login":"ryan-williams","id":465045,"avatar_url":"https://avatars.githubusercontent.com/u/465045?v=3","gravatar_id":"","url":"https://api.github.com/users/ryan-williams","html_url":"https://github.com/ryan-williams","followers_url":"https://api.github.com/users/ryan-williams/followers","following_url":"https://api.github.com/users/ryan-williams/following{/other_user}","gists_url":"https://api.github.com/users/ryan-williams/gists{/gist_id}","starred_url":"https://api.github.com/users/ryan-williams/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryan-williams/subscriptions","organizations_url":"https://api.github.com/users/ryan-williams/orgs","repos_url":"https://api.github.com/users/ryan-williams/repos","events_url":"https://api.github.com/users/ryan-williams/events{/privacy}","received_events_url":"https://api.github.com/users/ryan-williams/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-11-17T17:57:41Z","updated_at":"2016-11-21T16:59:20Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1277","html_url":"https://github.com/bigdatagenomics/adam/pull/1277","diff_url":"https://github.com/bigdatagenomics/adam/pull/1277.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/1277.patch"},"body":"I recently factored a small library for parsing string-representations of (possibly open-ended, e.g. `chr1`, `chr1:100-`) loci ranges out of guacamole and over to https://github.com/hammerlab/genomic-loci, because I was preparing to use it across a few of my projects, and in particular wanted it plus adam-core's `loadIndexedBam` functionality, which this PR adds.\r\n\r\n@fnothaft you mentioned there is some similar loci-parsing code laying around somewhere in BDG, lmk if I should find/consider it instead / in addition to this."},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/261998724","html_url":"https://github.com/bigdatagenomics/adam/pull/1277#issuecomment-261998724","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1277","id":261998724,"user":{"login":"heuermh","id":35293,"avatar_url":"https://avatars.githubusercontent.com/u/35293?v=3","gravatar_id":"","url":"https://api.github.com/users/heuermh","html_url":"https://github.com/heuermh","followers_url":"https://api.github.com/users/heuermh/followers","following_url":"https://api.github.com/users/heuermh/following{/other_user}","gists_url":"https://api.github.com/users/heuermh/gists{/gist_id}","starred_url":"https://api.github.com/users/heuermh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heuermh/subscriptions","organizations_url":"https://api.github.com/users/heuermh/orgs","repos_url":"https://api.github.com/users/heuermh/repos","events_url":"https://api.github.com/users/heuermh/events{/privacy}","received_events_url":"https://api.github.com/users/heuermh/received_events","type":"User","site_admin":false},"created_at":"2016-11-21T16:59:20Z","updated_at":"2016-11-21T16:59:20Z","body":"While I am supportive of the functionality proposed here, I would have to -1 it as is with the new dependency.  For better or worse, we need to cross-build for Spark 1.x/2.x and Scala 2.10/2.11 and so need upstream dependencies to do the same.\r\n\r\nWould there be much of a performance hit to transform\r\n`ParsedLoci` &rarr; `Iterable[ReferenceRegion]` &rarr; `Iterable[LocatableReferenceRegion]`\r\n\r\nas compared to\r\n`ParsedLoci` &rarr; `LociSet` &rarr; `lociSet.toHtsJDKIntervals`?"}}
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