{"action":"opened","issue":{"url":"https://api.github.com/repos/CSB5/lofreq/issues/7","labels_url":"https://api.github.com/repos/CSB5/lofreq/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/CSB5/lofreq/issues/7/comments","events_url":"https://api.github.com/repos/CSB5/lofreq/issues/7/events","html_url":"https://github.com/CSB5/lofreq/issues/7","id":54968667,"number":7,"title":"Handling of overlapping paired-end reads","user":{"login":"andreas-wilm","id":1095945,"avatar_url":"https://avatars.githubusercontent.com/u/1095945?v=3","gravatar_id":"","url":"https://api.github.com/users/andreas-wilm","html_url":"https://github.com/andreas-wilm","followers_url":"https://api.github.com/users/andreas-wilm/followers","following_url":"https://api.github.com/users/andreas-wilm/following{/other_user}","gists_url":"https://api.github.com/users/andreas-wilm/gists{/gist_id}","starred_url":"https://api.github.com/users/andreas-wilm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andreas-wilm/subscriptions","organizations_url":"https://api.github.com/users/andreas-wilm/orgs","repos_url":"https://api.github.com/users/andreas-wilm/repos","events_url":"https://api.github.com/users/andreas-wilm/events{/privacy}","received_events_url":"https://api.github.com/users/andreas-wilm/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/CSB5/lofreq/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":{"login":"andreas-wilm","id":1095945,"avatar_url":"https://avatars.githubusercontent.com/u/1095945?v=3","gravatar_id":"","url":"https://api.github.com/users/andreas-wilm","html_url":"https://github.com/andreas-wilm","followers_url":"https://api.github.com/users/andreas-wilm/followers","following_url":"https://api.github.com/users/andreas-wilm/following{/other_user}","gists_url":"https://api.github.com/users/andreas-wilm/gists{/gist_id}","starred_url":"https://api.github.com/users/andreas-wilm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andreas-wilm/subscriptions","organizations_url":"https://api.github.com/users/andreas-wilm/orgs","repos_url":"https://api.github.com/users/andreas-wilm/repos","events_url":"https://api.github.com/users/andreas-wilm/events{/privacy}","received_events_url":"https://api.github.com/users/andreas-wilm/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2015-01-21T02:13:18Z","updated_at":"2015-01-21T02:13:18Z","closed_at":null,"body":"Ideally overlapping paired-end reads shouldn't be counted twice. This could be achieved by proper post-processing (e.g. [SeqPrep](https://github.com/jstjohn/SeqPrep) and single-end mapping for merged pairs) or internally in LoFreq by making use of samtools \"read-pair overlap detection\".[Problem with the latter is that it [bumps up one quality and sets the other to zero](https://sourceforge.net/p/samtools/mailman/message/33063758/) instead of just swallowing the base."}}