{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/895","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/895/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/895/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/895/events","html_url":"https://github.com/bigdatagenomics/adam/pull/895","id":120635444,"number":895,"title":"Added is* genotype methods from HTS-JDK Genotype to RichGenotype","user":{"login":"NeillGibson","id":15608993,"avatar_url":"https://avatars.githubusercontent.com/u/15608993?v=3","gravatar_id":"","url":"https://api.github.com/users/NeillGibson","html_url":"https://github.com/NeillGibson","followers_url":"https://api.github.com/users/NeillGibson/followers","following_url":"https://api.github.com/users/NeillGibson/following{/other_user}","gists_url":"https://api.github.com/users/NeillGibson/gists{/gist_id}","starred_url":"https://api.github.com/users/NeillGibson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NeillGibson/subscriptions","organizations_url":"https://api.github.com/users/NeillGibson/orgs","repos_url":"https://api.github.com/users/NeillGibson/repos","events_url":"https://api.github.com/users/NeillGibson/events{/privacy}","received_events_url":"https://api.github.com/users/NeillGibson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-12-06T13:43:18Z","updated_at":"2015-12-07T21:17:45Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/895","html_url":"https://github.com/bigdatagenomics/adam/pull/895","diff_url":"https://github.com/bigdatagenomics/adam/pull/895.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/895.patch"},"body":"I added the is* genotype methods from HTS-JDK Genotype to Adam RichGenotype. \r\nThis makes it easier to filter on a genotypeRDD.\r\nCompare for instance \r\n`genotypeRDD.filter(_.isHom)`\r\nto\r\n`genotypeRDD.filter(gt => (gt.getType = GenotypeType.HOM_REF) || (gt.getType = GenotypeType.HOM_ALT)  )` \r\n\r\nThese methods are copied almost exactly from from\r\nhttps://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/variant/variantcontext/Genotype.java#L230\r\n\r\nI did not add `isMixed` and `isAvailable` since Adam seems to handle these Genotypes the same as GenotypeType.NO_CALL\r\n "},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/162666498","html_url":"https://github.com/bigdatagenomics/adam/pull/895#issuecomment-162666498","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/895","id":162666498,"user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"created_at":"2015-12-07T21:17:45Z","updated_at":"2015-12-07T21:17:45Z","body":"Code LGTM; will look at the Jenkins logs."}}