{"action":"created","issue":{"url":"https://api.github.com/repos/cancerit/CaVEMan/issues/40","labels_url":"https://api.github.com/repos/cancerit/CaVEMan/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/cancerit/CaVEMan/issues/40/comments","events_url":"https://api.github.com/repos/cancerit/CaVEMan/issues/40/events","html_url":"https://github.com/cancerit/CaVEMan/issues/40","id":101371443,"number":40,"title":"no calls gives unusual file sets ","user":{"login":"keiranmraine","id":3740323,"avatar_url":"https://avatars.githubusercontent.com/u/3740323?v=3","gravatar_id":"","url":"https://api.github.com/users/keiranmraine","html_url":"https://github.com/keiranmraine","followers_url":"https://api.github.com/users/keiranmraine/followers","following_url":"https://api.github.com/users/keiranmraine/following{/other_user}","gists_url":"https://api.github.com/users/keiranmraine/gists{/gist_id}","starred_url":"https://api.github.com/users/keiranmraine/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keiranmraine/subscriptions","organizations_url":"https://api.github.com/users/keiranmraine/orgs","repos_url":"https://api.github.com/users/keiranmraine/repos","events_url":"https://api.github.com/users/keiranmraine/events{/privacy}","received_events_url":"https://api.github.com/users/keiranmraine/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-17T08:47:58Z","updated_at":"2015-11-26T13:55:20Z","closed_at":null,"body":"If CaVEMan gives no calls during the estep you get a full set of `*.muts.vcf` files but no `*.snps.vcf`.\r\n\r\nThis causes the `mergeCavemanResults` script to fail.\r\n\r\nNot sure how this should be handled ot classified as the data is of no use but a clean run with a warning would be helpful.  I encountered this when running an WXS pair from cghub where it appears the tumour and normals don't have any common coverage."},"comment":{"url":"https://api.github.com/repos/cancerit/CaVEMan/issues/comments/159921647","html_url":"https://github.com/cancerit/CaVEMan/issues/40#issuecomment-159921647","issue_url":"https://api.github.com/repos/cancerit/CaVEMan/issues/40","id":159921647,"user":{"login":"drjsanger","id":7935268,"avatar_url":"https://avatars.githubusercontent.com/u/7935268?v=3","gravatar_id":"","url":"https://api.github.com/users/drjsanger","html_url":"https://github.com/drjsanger","followers_url":"https://api.github.com/users/drjsanger/followers","following_url":"https://api.github.com/users/drjsanger/following{/other_user}","gists_url":"https://api.github.com/users/drjsanger/gists{/gist_id}","starred_url":"https://api.github.com/users/drjsanger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drjsanger/subscriptions","organizations_url":"https://api.github.com/users/drjsanger/orgs","repos_url":"https://api.github.com/users/drjsanger/repos","events_url":"https://api.github.com/users/drjsanger/events{/privacy}","received_events_url":"https://api.github.com/users/drjsanger/received_events","type":"User","site_admin":false},"created_at":"2015-11-26T13:55:20Z","updated_at":"2015-11-26T13:55:20Z","body":"Unless CaVEMan silently failed between opening and writing the header to the muts file and doing the same for the snps fil I can't see how this could be possible. Is it still replicatable? "}}