{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/697","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/697/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/697/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/697/events","html_url":"https://github.com/broadinstitute/picard/pull/697","id":194184842,"number":697,"title":"Support in-line skips and molecular barcodes.","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":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-12-07T22:06:31Z","updated_at":"2016-12-08T16:07:46Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/697","html_url":"https://github.com/broadinstitute/picard/pull/697","diff_url":"https://github.com/broadinstitute/picard/pull/697.diff","patch_url":"https://github.com/broadinstitute/picard/pull/697.patch"},"body":"Solves issue https://github.com/broadinstitute/picard/issues/688\r\n\r\nThe phasing and pre-phasing metrics need all template cycles, including those that are marked as skips or molecular barcodes when the latter two are in-line in the reads.  I have not solved the case where we have both skips/molecular-barcodes in the index reads AND inline in the templates.  I added an option (`INCLUDE_SKIPS_AND_MOLECULAR_BARCODES`) that converts each skip or molecular barcode descriptor to a template descriptor for the purposes of `CollectIlluminaLaneMetrics`.\r\n\r\n@yfarjoun want to take a look?\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/265778682","html_url":"https://github.com/broadinstitute/picard/pull/697#issuecomment-265778682","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/697","id":265778682,"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":"2016-12-08T16:07:46Z","updated_at":"2016-12-08T16:07:46Z","body":"To do:\r\n- [ ] add a test (or two)"}}
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