{"action":"created","issue":{"url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/17","repository_url":"https://api.github.com/repos/Ensembl/Bio-HTS","labels_url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/17/comments","events_url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/17/events","html_url":"https://github.com/Ensembl/Bio-HTS/issues/17","id":155512774,"number":17,"title":"Memory leak: Bio::DB::HTS::Tabix - very reproducible","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},"labels":[{"url":"https://api.github.com/repos/Ensembl/Bio-HTS/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"andrewyatz","id":178457,"avatar_url":"https://avatars.githubusercontent.com/u/178457?v=3","gravatar_id":"","url":"https://api.github.com/users/andrewyatz","html_url":"https://github.com/andrewyatz","followers_url":"https://api.github.com/users/andrewyatz/followers","following_url":"https://api.github.com/users/andrewyatz/following{/other_user}","gists_url":"https://api.github.com/users/andrewyatz/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewyatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewyatz/subscriptions","organizations_url":"https://api.github.com/users/andrewyatz/orgs","repos_url":"https://api.github.com/users/andrewyatz/repos","events_url":"https://api.github.com/users/andrewyatz/events{/privacy}","received_events_url":"https://api.github.com/users/andrewyatz/received_events","type":"User","site_admin":false},"milestone":null,"comments":14,"created_at":"2016-05-18T14:16:29Z","updated_at":"2016-05-20T13:51:37Z","closed_at":null,"body":"Use the following small bit of code to reproduce with a tabix indexed BED file:\r\n\r\n````\r\n#!/usr/bin/perl\r\nuse strict;\r\nuse Bio::DB::HTS::Tabix;\r\n\r\nmy ($file, $search, $iterations) = @ARGV;\r\n\r\nmy $brass_np = Bio::DB::HTS::Tabix->new(filename => $file);\r\n\r\nfor(0..$iterations) {\r\n  my $iter = $brass_np->query($search);\r\n  while(my $record = $iter->next){ }\r\n}\r\n\r\n````\r\n\r\nExample runs (coordinate must hit records):\r\n\r\n````\r\n$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 1\r\n102848k maxresident\r\n$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 10\r\n108128k maxresident\r\n$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 100\r\n160880k maxresident\r\n$ /usr/bin/time -f '%Mk maxresident' perl htsTabix_mem.pl test.bed.gz 1:9551-10140 1000\r\n688240k maxresident\r\n````\r\n\r\nSeems a very similar problem to `Bio::DB::HTS::Faidx`\r\n\r\nThis is pretty critical as we've discovered this in the middle of a pre-release test cycle"},"comment":{"url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/comments/220610999","html_url":"https://github.com/Ensembl/Bio-HTS/issues/17#issuecomment-220610999","issue_url":"https://api.github.com/repos/Ensembl/Bio-HTS/issues/17","id":220610999,"user":{"login":"rishidev","id":5764069,"avatar_url":"https://avatars.githubusercontent.com/u/5764069?v=3","gravatar_id":"","url":"https://api.github.com/users/rishidev","html_url":"https://github.com/rishidev","followers_url":"https://api.github.com/users/rishidev/followers","following_url":"https://api.github.com/users/rishidev/following{/other_user}","gists_url":"https://api.github.com/users/rishidev/gists{/gist_id}","starred_url":"https://api.github.com/users/rishidev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rishidev/subscriptions","organizations_url":"https://api.github.com/users/rishidev/orgs","repos_url":"https://api.github.com/users/rishidev/repos","events_url":"https://api.github.com/users/rishidev/events{/privacy}","received_events_url":"https://api.github.com/users/rishidev/received_events","type":"User","site_admin":false},"created_at":"2016-05-20T13:51:37Z","updated_at":"2016-05-20T13:51:37Z","body":"Thanks Andy"}}
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