{"action":"opened","number":36,"pull_request":{"url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/pulls/36","id":90981613,"html_url":"https://github.com/Ensembl/Bio-DB-HTS/pull/36","diff_url":"https://github.com/Ensembl/Bio-DB-HTS/pull/36.diff","patch_url":"https://github.com/Ensembl/Bio-DB-HTS/pull/36.patch","issue_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/issues/36","number":36,"state":"open","locked":false,"title":"Create a way to Tabix query against chr containing ':'","user":{"login":"keiranmraine","id":3740323,"avatar_url":"https://avatars.githubusercontent.com/u/3740323?v=3","gravatar_id":"","url":"https://api.github.com/users/keiranmraine","html_url":"https://github.com/keiranmraine","followers_url":"https://api.github.com/users/keiranmraine/followers","following_url":"https://api.github.com/users/keiranmraine/following{/other_user}","gists_url":"https://api.github.com/users/keiranmraine/gists{/gist_id}","starred_url":"https://api.github.com/users/keiranmraine/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keiranmraine/subscriptions","organizations_url":"https://api.github.com/users/keiranmraine/orgs","repos_url":"https://api.github.com/users/keiranmraine/repos","events_url":"https://api.github.com/users/keiranmraine/events{/privacy}","received_events_url":"https://api.github.com/users/keiranmraine/received_events","type":"User","site_admin":false},"body":"Hi,\r\n\r\nThe HLA contigs in human GRCh38 have names like 'HLA-A*01:01:01:01'.  Constructing a query against these results in:\r\n\r\n```\r\nHLA-A*01:01:01:01:0-13503\r\nEVAL_ERROR: You must specify a region in the format chr, chr:start or chr:start-end at /.../local/lib/perl5/x86_64-linux-thread-multi/Bio/DB/HTS/Tabix.pm line 64.\r\n```\r\n\r\nThis is a failure in the way the region format checking is carried out.\r\n\r\nThe C tabix command line works with one caveat, if the chromosome contains `:` then it must be followed with `:` when addressed on it's own:\r\n\r\n```\r\n$ tabix test.tsv.gz 'HLA-A*01:01:01:01:1-50'\r\nHLA-A*01:01:01:01\t1\t500\t0.65\r\n$ tabix test.tsv.gz 'HLA-A*01:01:01:01:1'\r\nHLA-A*01:01:01:01\t1\t500\t0.65\r\n$ tabix test.tsv.gz 'HLA-A*01:01:01:01:'\r\nHLA-A*01:01:01:01\t1\t500\t0.65\r\n$ tabix test.tsv.gz 'HLA-A*01:01:01:01'\r\n# no result\r\n```\r\n\r\nThis PR adds a new tabix method of `query_full` which allows the calling code to specify the elements of a region rather than a string, and then constructs a valid one to pass to the C layer.\r\n\r\nAs there is overlap, the original `query` function calls the `query_full` method for the common components.\r\n\r\nI would recommend extending the error messages to indicate that this is a possible cause of failure to parse as well as deprecating the original `query` function.\r\n\r\nAlternatively the original pattern match in `query` could be modified, however the only restriction in contig naming I'm aware of is whitespace.","created_at":"2016-10-26T11:01:38Z","updated_at":"2016-10-26T11:01:38Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/pulls/36/commits","review_comments_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/pulls/36/comments","review_comment_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/pulls/comments{/number}","comments_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/issues/36/comments","statuses_url":"https://api.github.com/repos/Ensembl/Bio-DB-HTS/statuses/d4f9df5e1cfff94a6bda18931f7b68e107079998","head":{"label":"keiranmraine:hotfix/2.5.1","ref":"hotfix/2.5.1","sha":"d4f9df5e1cfff94a6bda18931f7b68e107079998","user":{"login":"keiranmraine","id":3740323,"avatar_url":"https://avatars.githubusercontent.com/u/3740323?v=3","gravatar_id":"","url":"https://api.github.com/users/keiranmraine","html_url":"https://github.com/keiranmraine","followers_url":"https://api.github.com/users/keiranmraine/followers","following_url":"https://api.github.com/users/keiranmraine/following{/other_user}","gists_url":"https://api.github.com/users/keiranmraine/gists{/gist_id}","starred_url":"https://api.github.com/users/keiranmraine/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keiranmraine/subscriptions","organizations_url":"https://api.github.com/users/keiranmraine/orgs","repos_url":"https://api.github.com/users/keiranmraine/repos","events_url":"https://api.github.com/users/keiranmraine/events{/privacy}","received_events_url":"https://api.github.com/users/keiranmraine/received_events","type":"User","site_admin":false},"repo":{"id":71990167,"name":"Bio-DB-HTS","full_name":"keiranmraine/Bio-DB-HTS","owner":{"login":"keiranmraine","id":3740323,"avatar_url":"https://avatars.githubusercontent.com/u/3740323?v=3","gravatar_id":"","url":"https://api.github.com/users/keiranmraine","html_url":"https://github.com/keiranmraine","followers_url":"https://api.github.com/users/keiranmraine/followers","following_url":"https://api.github.com/users/keiranmraine/following{/other_user}","gists_url":"https://api.github.com/users/keiranmraine/gists{/gist_id}","starred_url":"https://api.github.com/users/keiranmraine/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/keiranmraine/subscriptions","organizations_url":"https://api.github.com/users/keiranmraine/orgs","repos_url":"https://api.github.com/users/keiranmraine/repos","events_url":"https://api.github.com/users/keiranmraine/events{/privacy}","received_events_url":"https://api.github.com/users/keiranmraine/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/keiranmraine/Bio-DB-HTS","description":"Git 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