{"action":"created","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3028","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3028/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3028/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3028/events","html_url":"https://github.com/Homebrew/homebrew-science/pull/3028","id":117012295,"number":3028,"title":"Freebayes 1.0.1 (new formula)","user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Homebrew/homebrew-science/labels/Bioinformatics","name":"Bioinformatics","color":"207de5"},{"url":"https://api.github.com/repos/Homebrew/homebrew-science/labels/New%20formula","name":"New formula","color":"444444"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-11-15T19:25:19Z","updated_at":"2015-11-20T09:21:53Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/pulls/3028","html_url":"https://github.com/Homebrew/homebrew-science/pull/3028","diff_url":"https://github.com/Homebrew/homebrew-science/pull/3028.diff","patch_url":"https://github.com/Homebrew/homebrew-science/pull/3028.patch"},"body":"FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.\r\n\r\nFreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment. This model is a straightforward generalization of previous ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on alignments. This method avoids one of the core problems with alignment-based variant detection--- that identical sequences may have multiple possible alignments:\r\n\r\nFreeBayes uses short-read alignments (BAM files with Phred+33 encoded quality scores, now standard) for any number of individuals from a population and a reference genome (in FASTA format) to determine the most-likely combination of genotypes for the population at each position in the reference. It reports positions which it finds putatively polymorphic in variant call file (VCF) format. It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis."},"comment":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/comments/158334034","html_url":"https://github.com/Homebrew/homebrew-science/pull/3028#issuecomment-158334034","issue_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3028","id":158334034,"user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"created_at":"2015-11-20T09:21:53Z","updated_at":"2015-11-20T09:21:53Z","body":"```\r\nError: GitHub API rate limit exceeded for 208.78.110.199. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)\r\nTry again in 42 minutes 34 seconds, or create a personal access token:\r\n  https://github.com/settings/tokens/new?scopes=&description=Homebrew\r\nand then set the token as: HOMEBREW_GITHUB_API_TOKEN\r\n```\r\n"}}