{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/355","labels_url":"https://api.github.com/repos/samtools/samtools/issues/355/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/355/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/355/events","html_url":"https://github.com/samtools/samtools/issues/355","id":59110796,"number":355,"title":"wgsim: Please add is_flip (the orientation) to the read ID","user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jkbonfield","id":2210525,"avatar_url":"https://avatars.githubusercontent.com/u/2210525?v=3","gravatar_id":"","url":"https://api.github.com/users/jkbonfield","html_url":"https://github.com/jkbonfield","followers_url":"https://api.github.com/users/jkbonfield/followers","following_url":"https://api.github.com/users/jkbonfield/following{/other_user}","gists_url":"https://api.github.com/users/jkbonfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jkbonfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkbonfield/subscriptions","organizations_url":"https://api.github.com/users/jkbonfield/orgs","repos_url":"https://api.github.com/users/jkbonfield/repos","events_url":"https://api.github.com/users/jkbonfield/events{/privacy}","received_events_url":"https://api.github.com/users/jkbonfield/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-02-26T17:51:10Z","updated_at":"2015-07-08T17:32:48Z","closed_at":null,"body":"The read ID output by wgsim does not include the orientation of the read, `is_flip`. It would be really useful to include the orientation.\r\n\r\nA read ID currently has six fields separated by underscores\r\n`@0_80_129_0:0:0_0:0:0_e/1`\r\n\r\nCan we add a seventh field that specifies `1` for reverse complement and `0` otherwise? I'd be happy to submit a pull request if you agree.\r\n`@0_80_129_0:0:0_0:0:0_e_0/1` or `@0_80_129_0:0:0_0:0:0_e_1/1`\r\n\r\nhttps://github.com/samtools/samtools/blob/develop/misc/wgsim.c#L345-L347\r\n```c\r\n                fprintf(fpo[j], \"@%s_%u_%u_%d:%d:%d_%d:%d:%d_%llx/%d\\n\", ks->name.s, ext_coor[0]+1, ext_coor[1]+1,\r\n                        n_err[0], n_sub[0], n_indel[0], n_err[1], n_sub[1], n_indel[1],\r\n                        (long long)ii, j==0? is_flip+1 : 2-is_flip);\r\n```"},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/119671767","html_url":"https://github.com/samtools/samtools/issues/355#issuecomment-119671767","issue_url":"https://api.github.com/repos/samtools/samtools/issues/355","id":119671767,"user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"created_at":"2015-07-08T17:32:48Z","updated_at":"2015-07-08T17:32:48Z","body":"Which is the canonical version of wgsim, `samtools/samtools` or `lh3/wgsim`?"}}