{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/53181845","id":53181845,"diff_hunk":"@@ -114,7 +114,7 @@ protected Object doWork() {\n             validator.setBisulfiteSequenced(IS_BISULFITE_SEQUENCED);\n         }\n         if (VALIDATE_INDEX) {\n-            validator.setValidateIndex(VALIDATE_INDEX);\n+            validator.setIndexValidationStringency(BamIndexValidator.IndexValidationStringency.EXHAUSTIVE);","path":"src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ValidateSamFile.java","position":5,"original_position":5,"commit_id":"db98950071698c6944f9940f60c03372bd2a2ecd","original_commit_id":"db98950071698c6944f9940f60c03372bd2a2ecd","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"body":"AFAIK, index validation was binary before, and the concept of stringency level didn't exist. It was introduced by https://github.com/samtools/htsjdk/pull/397. I think the idea was to introduce a less exhaustive and faster validation level. So I think exhaustive is the equivalent of what we used to do. Whether we want to relax that is another question. See https://github.com/broadinstitute/picard/issues/346.","created_at":"2016-02-17T15:41:31Z","updated_at":"2016-02-17T15:41:31Z","html_url":"https://github.com/broadinstitute/gatk/pull/1469#discussion_r53181845","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1469","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/53181845"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1469#discussion_r53181845"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1469"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1469","id":58214760,"html_url":"https://github.com/broadinstitute/gatk/pull/1469","diff_url":"https://github.com/broadinstitute/gatk/pull/1469.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1469.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1469","number":1469,"state":"open","locked":false,"title":"Hadoop-BAM and htsjdk upgrades, Spark tool changes.","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"body":"Requires upgrades to Hadoop-BAM (not yet released) and htsjdk.\r\n\r\nFixes https://github.com/broadinstitute/gatk/issues/1346, https://github.com/broadinstitute/gatk/issues/1261, https://github.com/broadinstitute/gatk/issues/1175, https://github.com/broadinstitute/gatk/issues/1326, https://github.com/broadinstitute/gatk/issues/1259, and much of the underlying code for https://github.com/broadinstitute/gatk/issues/1270, which will be enabled in a separate 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