{"action":"created","comment":{"url":"https://api.github.com/repos/PROSIC/libprosic/pulls/comments/204433464","pull_request_review_id":139513154,"id":204433464,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwNDQzMzQ2NA==","diff_hunk":"@@ -658,6 +643,7 @@ fn test_sc_bulk_indel() {\n     call_single_cell_bulk(\"test_sc_bulk_indel\", true, \"chr1\");\n     let mut call = load_call(\"test_sc_bulk_indel\");\n     check_info_float(&mut call, b\"CONTROL_AF\", 0.0, 0.0);\n+    // TODO case AF seems to be > 0, also from looking at IGV. Are you sure the test case is correct?","path":"tests/lib.rs","position":260,"original_position":251,"commit_id":"8d318fd8556079cc87f08c3734b24ed66acab418","original_commit_id":"abf168eff435c21b4fa604848629a36e61489eb3","user":{"login":"dlaehnemann","id":1379875,"node_id":"MDQ6VXNlcjEzNzk4NzU=","avatar_url":"https://avatars1.githubusercontent.com/u/1379875?v=4","gravatar_id":"","url":"https://api.github.com/users/dlaehnemann","html_url":"https://github.com/dlaehnemann","followers_url":"https://api.github.com/users/dlaehnemann/followers","following_url":"https://api.github.com/users/dlaehnemann/following{/other_user}","gists_url":"https://api.github.com/users/dlaehnemann/gists{/gist_id}","starred_url":"https://api.github.com/users/dlaehnemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dlaehnemann/subscriptions","organizations_url":"https://api.github.com/users/dlaehnemann/orgs","repos_url":"https://api.github.com/users/dlaehnemann/repos","events_url":"https://api.github.com/users/dlaehnemann/events{/privacy}","received_events_url":"https://api.github.com/users/dlaehnemann/received_events","type":"User","site_admin":false},"body":"Done, let's see if this passes.","created_at":"2018-07-23T14:57:10Z","updated_at":"2018-07-23T14:57:10Z","html_url":"https://github.com/PROSIC/libprosic/pull/38#discussion_r204433464","pull_request_url":"https://api.github.com/repos/PROSIC/libprosic/pulls/38","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/PROSIC/libprosic/pulls/comments/204433464"},"html":{"href":"https://github.com/PROSIC/libprosic/pull/38#discussion_r204433464"},"pull_request":{"href":"https://api.github.com/repos/PROSIC/libprosic/pulls/38"}},"in_reply_to_id":204340019},"pull_request":{"url":"https://api.github.com/repos/PROSIC/libprosic/pulls/38","id":203148163,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAzMTQ4MTYz","html_url":"https://github.com/PROSIC/libprosic/pull/38","diff_url":"https://github.com/PROSIC/libprosic/pull/38.diff","patch_url":"https://github.com/PROSIC/libprosic/pull/38.patch","issue_url":"https://api.github.com/repos/PROSIC/libprosic/issues/38","number":38,"state":"open","locked":false,"title":"Use binary MAPQ if requested","user":{"login":"johanneskoester","id":1858646,"node_id":"MDQ6VXNlcjE4NTg2NDY=","avatar_url":"https://avatars1.githubusercontent.com/u/1858646?v=4","gravatar_id":"","url":"https://api.github.com/users/johanneskoester","html_url":"https://github.com/johanneskoester","followers_url":"https://api.github.com/users/johanneskoester/followers","following_url":"https://api.github.com/users/johanneskoester/following{/other_user}","gists_url":"https://api.github.com/users/johanneskoester/gists{/gist_id}","starred_url":"https://api.github.com/users/johanneskoester/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johanneskoester/subscriptions","organizations_url":"https://api.github.com/users/johanneskoester/orgs","repos_url":"https://api.github.com/users/johanneskoester/repos","events_url":"https://api.github.com/users/johanneskoester/events{/privacy}","received_events_url":"https://api.github.com/users/johanneskoester/received_events","type":"User","site_admin":false},"body":"It turns out that MAPQ is biased towards lower MAPQ for non-ref fragments when observing SVs. Hence, when considering MAPQ in out latent variable model, we always get a bias towards the ref allele, which generates both false negatives and false positives (either missing a variant in tumor or in normal).\r\n\r\nTo overcome this problem, we can binarize the MAPQ, taking the maximum observed (e.g. 60) for all reads with MAPQ > 0 and 0 otherwise. This works really well, giving superior precision-recall over all other callers.","created_at":"2018-07-23T08:45:28Z","updated_at":"2018-07-23T14:57:10Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d0747c7725437e70c48f4f20307f616d6453861e","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/PROSIC/libprosic/pulls/38/commits","review_comments_url":"https://api.github.com/repos/PROSIC/libprosic/pulls/38/comments","review_comment_url":"https://api.github.com/repos/PROSIC/libprosic/pulls/comments{/number}","comments_url":"https://api.github.com/repos/PROSIC/libprosic/issues/38/comments","statuses_url":"https://api.github.com/repos/PROSIC/libprosic/statuses/8d318fd8556079cc87f08c3734b24ed66acab418","head":{"label":"PROSIC:recalc-se-mapq","ref":"recalc-se-mapq","sha":"8d318fd8556079cc87f08c3734b24ed66acab418","user":{"login":"PROSIC","id":19840508,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE5ODQwNTA4","avatar_url":"https://avatars0.githubusercontent.com/u/19840508?v=4","gravatar_id":"","url":"https://api.github.com/users/PROSIC","html_url":"https://github.com/PROSIC","followers_url":"https://api.github.com/users/PROSIC/followers","following_url":"https://api.github.com/users/PROSIC/following{/other_user}","gists_url":"https://api.github.com/users/PROSIC/gists{/gist_id}","starred_url":"https://api.github.com/users/PROSIC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PROSIC/subscriptions","organizations_url":"https://api.github.com/users/PROSIC/orgs","repos_url":"https://api.github.com/users/PROSIC/repos","events_url":"https://api.github.com/users/PROSIC/events{/privacy}","received_events_url":"https://api.github.com/users/PROSIC/received_events","type":"Organization","site_admin":false},"repo":{"id":62696760,"node_id":"MDEwOlJlcG9zaXRvcnk2MjY5Njc2MA==","name":"libprosic","full_name":"PROSIC/libprosic","owner":{"login":"PROSIC","id":19840508,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE5ODQwNTA4","avatar_url":"https://avatars0.githubusercontent.com/u/19840508?v=4","gravatar_id":"","url":"https://api.github.com/users/PROSIC","html_url":"https://github.com/PROSIC","followers_url":"https://api.github.com/users/PROSIC/followers","following_url":"https://api.github.com/users/PROSIC/following{/other_user}","gists_url":"https://api.github.com/users/PROSIC/gists{/gist_id}","starred_url":"https://api.github.com/users/PROSIC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PROSIC/subscriptions","organizations_url":"https://api.github.com/users/PROSIC/orgs","repos_url":"https://api.github.com/users/PROSIC/repos","events_url":"https://api.github.com/users/PROSIC/events{/privacy}","received_events_url":"https://api.github.com/users/PROSIC/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/PROSIC/libprosic","description":"A 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