{"action":"created","issue":{"url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/90","labels_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/90/labels{/name}","comments_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/90/comments","events_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/90/events","html_url":"https://github.com/googlegenomics/dataflow-java/pull/90","id":84729343,"number":90,"title":"Added the CalculateCoverage pipeline/tests.","user":{"login":"Careyjmac","id":5719025,"avatar_url":"https://avatars.githubusercontent.com/u/5719025?v=3","gravatar_id":"","url":"https://api.github.com/users/Careyjmac","html_url":"https://github.com/Careyjmac","followers_url":"https://api.github.com/users/Careyjmac/followers","following_url":"https://api.github.com/users/Careyjmac/following{/other_user}","gists_url":"https://api.github.com/users/Careyjmac/gists{/gist_id}","starred_url":"https://api.github.com/users/Careyjmac/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Careyjmac/subscriptions","organizations_url":"https://api.github.com/users/Careyjmac/orgs","repos_url":"https://api.github.com/users/Careyjmac/repos","events_url":"https://api.github.com/users/Careyjmac/events{/privacy}","received_events_url":"https://api.github.com/users/Careyjmac/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-03T19:16:21Z","updated_at":"2015-06-03T19:33:50Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/googlegenomics/dataflow-java/pulls/90","html_url":"https://github.com/googlegenomics/dataflow-java/pull/90","diff_url":"https://github.com/googlegenomics/dataflow-java/pull/90.diff","patch_url":"https://github.com/googlegenomics/dataflow-java/pull/90.patch"},"body":"Pipeline for calculating read depth coverage for a given data set, with unit tests.\r\n\r\nFor each \"bucket\" in the given input references, this computes the average coverage (rounded to\r\nsix decimal places) across the bucket that 10%, 20%, 30%, etc. of the input ReadGroupsSets have\r\nfor each mapping quality of the reads (<10:Low(L), 10-29:Medium(M), >=30:High(H)) as well as\r\nthese same percentiles of ReadGroupSets for all reads regardless of mapping quality (Mapping\r\nquality All(A)).\r\n\r\nThere is also the option to change the number of quantiles accordingly (numQuantiles = 5 would\r\ngive you the minimum ReadGroupSet mean coverage for each and across all mapping qualities, the\r\n25th, 50th, and 75th percentiles, and the maximum of these values)."},"comment":{"url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/comments/108590375","html_url":"https://github.com/googlegenomics/dataflow-java/pull/90#issuecomment-108590375","issue_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/90","id":108590375,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2015-06-03T19:33:50Z","updated_at":"2015-06-03T19:33:50Z","body":"\n[![Coverage Status](https://coveralls.io/builds/2721691/badge)](https://coveralls.io/builds/2721691)\n\nCoverage increased (+3.56%) to 28.75% when pulling **93289a734ab0e274a61837b97d37468d24348681 on coveragePipeline** into **1f0ca31869c336bc7fb72b2176f4c27de83e6e54 on master**.\n"}}