{"action":"opened","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/5492","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5492/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5492/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5492/events","html_url":"https://github.com/broadinstitute/gatk/issues/5492","id":388495546,"node_id":"MDU6SXNzdWUzODg0OTU1NDY=","number":5492,"title":"ReadPosRankSumTest doesn't work for two deletions with one base in between","user":{"login":"davidbenjamin","id":8438890,"node_id":"MDQ6VXNlcjg0Mzg4OTA=","avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"labels":[{"id":649053840,"node_id":"MDU6TGFiZWw2NDkwNTM4NDA=","url":"https://api.github.com/repos/broadinstitute/gatk/labels/Annotations","name":"Annotations","color":"c5def5","default":false},{"id":153552584,"node_id":"MDU6TGFiZWwxNTM1NTI1ODQ=","url":"https://api.github.com/repos/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-07T03:52:40Z","updated_at":"2018-12-07T03:52:40Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"When `ReadPosRankSumTest.getReadPosition` encounters the second of two deletions with a single base in between it hits the following code:\r\n```\r\nif ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) {\r\n            return OptionalDouble.of(INVALID_ELEMENT_FROM_READ);\r\n}\r\n```\r\nwhich returns negative infinity.  Those with TCGA access can reproduce the issue by running on the TCGA exome pair ESCA-IG-A3YB-TP-NB at 15:34525804-34525810."}}
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