{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/668","repository_url":"https://api.github.com/repos/samtools/htsjdk","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/668/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/668/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/668/events","html_url":"https://github.com/samtools/htsjdk/pull/668","id":167251406,"number":668,"title":"Fix JexlMap and GenotypeJEXLContext NullPtrException","user":{"login":"SHuang-Broad","id":16310888,"avatar_url":"https://avatars.githubusercontent.com/u/16310888?v=3","gravatar_id":"","url":"https://api.github.com/users/SHuang-Broad","html_url":"https://github.com/SHuang-Broad","followers_url":"https://api.github.com/users/SHuang-Broad/followers","following_url":"https://api.github.com/users/SHuang-Broad/following{/other_user}","gists_url":"https://api.github.com/users/SHuang-Broad/gists{/gist_id}","starred_url":"https://api.github.com/users/SHuang-Broad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SHuang-Broad/subscriptions","organizations_url":"https://api.github.com/users/SHuang-Broad/orgs","repos_url":"https://api.github.com/users/SHuang-Broad/repos","events_url":"https://api.github.com/users/SHuang-Broad/events{/privacy}","received_events_url":"https://api.github.com/users/SHuang-Broad/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/samtools/htsjdk/labels/Review-party%20candidate","name":"Review-party candidate","color":"5319e7"}],"state":"open","locked":false,"assignee":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"assignees":[{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false}],"milestone":null,"comments":11,"created_at":"2016-07-24T20:06:20Z","updated_at":"2016-08-27T16:45:01Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/668","html_url":"https://github.com/samtools/htsjdk/pull/668","diff_url":"https://github.com/samtools/htsjdk/pull/668.diff","patch_url":"https://github.com/samtools/htsjdk/pull/668.patch"},"body":"### Description\r\n\r\n* `GenotypeJEXLContext.get()` currently potentially throws `NullPointerException`, triggered by a design choice in `Genotype.getFilters()`, which explicitly returns `null` (genotype considered to be filter passing in such case according to documentation). This fix temporarily fixes that exception (1st commit, by Louis).\r\n\r\n* Class `CommonInfo`, which holds \"Common utility routines for VariantContext and Genotype\", contains such a constant \r\n        \r\n        private static Set<String> NO_FILTERS = Collections.emptySet();\r\n\r\n    `VariantContext` uses this constant in its own `getFilters()` (it has a separate method `getFiltersMaybeNull()`), but `Genotype` doesn't use such constant. A choice has to be made to whether make `Genotype` resemble `VariantContext`'s behavior (a backward non-compatible change) or keep things as they are.\r\n\r\n* Some code re-organizing and whole bunch of todo's in `JEXLMap`, which must be resolved in the review rounds.\r\n\r\n\r\n### Checklist\r\n\r\n- [x] Code compiles correctly\r\n- [ ] New tests covering changes and new functionality\r\n- [x] All tests passing\r\n- [PartiallyDone] Extended the README / documentation, if necessary\r\n- [Possibly] Is not backward compatible (breaks binary or source compatibility)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/242927651","html_url":"https://github.com/samtools/htsjdk/pull/668#issuecomment-242927651","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/668","id":242927651,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2016-08-27T16:45:01Z","updated_at":"2016-08-27T16:45:01Z","body":"\n[![Coverage Status](https://coveralls.io/builds/7637599/badge)](https://coveralls.io/builds/7637599)\n\nCoverage increased (+0.09%) to 68.974% when pulling **dd4fc6082e3cd8ee74615c3941a7bdb7639893d0 on SHuang-Broad:sh_fix_GenotypeJEXLContext_nullptr** into **a31f6c84a409c599de5b991595cd5ac0daae3a45 on samtools:master**.\n"}}
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