GitHub PullRequestReviewCommentEvent at 2014-10-23 19:49:48
Repository: api-client-r
Actor: cassiedoll
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/comments/19302827","id":19302827,"diff_hunk":"@@ -0,0 +1,100 @@\n+\n+Reproducing Variant Annotation Results\n+---------------------------------------\n+\n+Below we compare the results of annotating variants via the [VariantAnnotation](http://www.bioconductor.org/packages/release/bioc/html/VariantAnnotation.html)  [BioConductor](http://www.bioconductor.org/) package.  We compare using data from 1,000 Genomes Phase 1 Variants:\n+* as parsed from a VCF file\n+* retrieved from the Google Genomics API\n+\n+### VCF Data\n+\n+First we read in the data from the VCF file:\n+```{r}\n+require(VariantAnnotation)\n+fl <- system.file(\"extdata\", \"chr22.vcf.gz\", package=\"VariantAnnotation\")\n+vcf <- readVcf(fl, \"hg19\")\n+vcf\n+```\n+\n+The file `chr22.vcf.gz` within package VariantAnnotation holds data for 5 of the 1,092 individuals in 1,000 Genomes, starting at position 50300078 and ending at position 50999964.\n+\n+`HG00096 HG00097 HG00099 HG00100 HG00101`\n+\n+### Google Genomics Data\n+\n+Important data differences to note:\n+ 1 VCF data is 1-based but data from the GA4GH APIs is 0-based, for more information see (https://www.biostars.org/p/84686/)","path":"inst/doc/VariantAnnotation-comparison-test.Rmd","position":26,"original_position":26,"commit_id":"5e171821475701684979b7bb63b890ec05dfff4b","original_commit_id":"5e171821475701684979b7bb63b890ec05dfff4b","user":{"login":"cassiedoll","id":6655977,"avatar_url":"https://avatars.githubusercontent.com/u/6655977?v=2","gravatar_id":"","url":"https://api.github.com/users/cassiedoll","html_url":"https://github.com/cassiedoll","followers_url":"https://api.github.com/users/cassiedoll/followers","following_url":"https://api.github.com/users/cassiedoll/following{/other_user}","gists_url":"https://api.github.com/users/cassiedoll/gists{/gist_id}","starred_url":"https://api.github.com/users/cassiedoll/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cassiedoll/subscriptions","organizations_url":"https://api.github.com/users/cassiedoll/orgs","repos_url":"https://api.github.com/users/cassiedoll/repos","events_url":"https://api.github.com/users/cassiedoll/events{/privacy}","received_events_url":"https://api.github.com/users/cassiedoll/received_events","type":"User","site_admin":false},"body":"these bullets aren't rendering correctly","created_at":"2014-10-23T19:49:48Z","updated_at":"2014-10-23T19:49:48Z","html_url":"https://github.com/googlegenomics/api-client-r/pull/11#discussion_r19302827","pull_request_url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/11","_links":{"self":{"href":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/comments/19302827"},"html":{"href":"https://github.com/googlegenomics/api-client-r/pull/11#discussion_r19302827"},"pull_request":{"href":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/11"}}},"pull_request":{"url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/11","id":23200569,"html_url":"https://github.com/googlegenomics/api-client-r/pull/11","diff_url":"https://github.com/googlegenomics/api-client-r/pull/11.diff","patch_url":"https://github.com/googlegenomics/api-client-r/pull/11.patch","issue_url":"https://api.github.com/repos/googlegenomics/api-client-r/issues/11","number":11,"state":"open","locked":false,"title":"An initial vignette for Variant Annotation.","user":{"login":"deflaux","id":1395500,"avatar_url":"https://avatars.githubusercontent.com/u/1395500?v=2","gravatar_id":"","url":"https://api.github.com/users/deflaux","html_url":"https://github.com/deflaux","followers_url":"https://api.github.com/users/deflaux/followers","following_url":"https://api.github.com/users/deflaux/following{/other_user}","gists_url":"https://api.github.com/users/deflaux/gists{/gist_id}","starred_url":"https://api.github.com/users/deflaux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deflaux/subscriptions","organizations_url":"https://api.github.com/users/deflaux/orgs","repos_url":"https://api.github.com/users/deflaux/repos","events_url":"https://api.github.com/users/deflaux/events{/privacy}","received_events_url":"https://api.github.com/users/deflaux/received_events","type":"User","site_admin":false},"body":"@siddharthab I also had to do a bit of the refactoring we discussed to make this work.  \r\n\r\nThe convert-to-BioConductor objects stuff is quick and dirty for now.  It will get better.","created_at":"2014-10-23T00:47:06Z","updated_at":"2014-10-23T19:49:48Z","closed_at":null,"merged_at":null,"merge_commit_sha":"9b80593d016ce080d40d8de61da76ec764016ea9","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/11/commits","review_comments_url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/11/comments","review_comment_url":"https://api.github.com/repos/googlegenomics/api-client-r/pulls/comments/{number}","comments_url":"https://api.github.com/repos/googlegenomics/api-client-r/issues/11/comments","statuses_url":"https://api.github.com/repos/googlegenomics/api-client-r/statuses/5e171821475701684979b7bb63b890ec05dfff4b","head":{"label":"deflaux:master","ref":"master","sha":"5e171821475701684979b7bb63b890ec05dfff4b","user":{"login":"deflaux","id":1395500,"avatar_url":"https://avatars.githubusercontent.com/u/1395500?v=2","gravatar_id":"","url":"https://api.github.com/users/deflaux","html_url":"https://github.com/deflaux","followers_url":"https://api.github.com/users/deflaux/followers","following_url":"https://api.github.com/users/deflaux/following{/other_user}","gists_url":"https://api.github.com/users/deflaux/gists{/gist_id}","starred_url":"https://api.github.com/users/deflaux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deflaux/subscriptions","organizations_url":"https://api.github.com/users/deflaux/orgs","repos_url":"https://api.github.com/users/deflaux/repos","events_url":"https://api.github.com/users/deflaux/events{/privacy}","received_events_url":"https://api.github.com/users/deflaux/received_events","type":"User","site_admin":false},"repo":{"id":24206600,"name":"api-client-r","full_name":"deflaux/api-client-r","owner":{"login":"deflaux","id":1395500,"avatar_url":"https://avatars.githubusercontent.com/u/1395500?v=2","gravatar_id":"","url":"https://api.github.com/users/deflaux","html_url":"https://github.com/deflaux","followers_url":"https://api.github.com/users/deflaux/followers","following_url":"https://api.github.com/users/deflaux/following{/other_user}","gists_url":"https://api.github.com/users/deflaux/gists{/gist_id}","starred_url":"https://api.github.com/users/deflaux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deflaux/subscriptions","organizations_url":"https://api.github.com/users/deflaux/orgs","repos_url":"https://api.github.com/users/deflaux/repos","events_url":"https://api.github.com/users/deflaux/events{/privacy}","received_events_url":"https://api.github.com/users/deflaux/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/deflaux/api-client-r","description":"Provides 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