{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/fx_tools/issues/1","labels_url":"https://api.github.com/repos/seqan/fx_tools/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/seqan/fx_tools/issues/1/comments","events_url":"https://api.github.com/repos/seqan/fx_tools/issues/1/events","html_url":"https://github.com/seqan/fx_tools/pull/1","id":59416456,"number":1,"title":"[FEATURE] tools to compute variant density and basepair-accurate read depth","user":{"login":"weese","id":1064949,"avatar_url":"https://avatars.githubusercontent.com/u/1064949?v=3","gravatar_id":"","url":"https://api.github.com/users/weese","html_url":"https://github.com/weese","followers_url":"https://api.github.com/users/weese/followers","following_url":"https://api.github.com/users/weese/following{/other_user}","gists_url":"https://api.github.com/users/weese/gists{/gist_id}","starred_url":"https://api.github.com/users/weese/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/weese/subscriptions","organizations_url":"https://api.github.com/users/weese/orgs","repos_url":"https://api.github.com/users/weese/repos","events_url":"https://api.github.com/users/weese/events{/privacy}","received_events_url":"https://api.github.com/users/weese/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"esiragusa","id":172085,"avatar_url":"https://avatars.githubusercontent.com/u/172085?v=3","gravatar_id":"","url":"https://api.github.com/users/esiragusa","html_url":"https://github.com/esiragusa","followers_url":"https://api.github.com/users/esiragusa/followers","following_url":"https://api.github.com/users/esiragusa/following{/other_user}","gists_url":"https://api.github.com/users/esiragusa/gists{/gist_id}","starred_url":"https://api.github.com/users/esiragusa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/esiragusa/subscriptions","organizations_url":"https://api.github.com/users/esiragusa/orgs","repos_url":"https://api.github.com/users/esiragusa/repos","events_url":"https://api.github.com/users/esiragusa/events{/privacy}","received_events_url":"https://api.github.com/users/esiragusa/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-03-01T20:43:21Z","updated_at":"2015-03-01T21:13:25Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/seqan/fx_tools/pulls/1","html_url":"https://github.com/seqan/fx_tools/pull/1","diff_url":"https://github.com/seqan/fx_tools/pull/1.diff","patch_url":"https://github.com/seqan/fx_tools/pull/1.patch"},"body":"I just reopened the PR #868 in the new fx_tools repo (#868 will be closed).\r\n\r\nI've finished a first version of tabix support which in conjunction with any chromosomal file format, e.g. VCF allows range queries on the file itself. To use the tabix index one has to compress the tab-delimited text file with bgzip (.gz) and index it with tabix (.gz.tbi).\r\n\r\nI added a simple demo to show how it works and a test.\r\n\r\n```\r\n./bin/demo_tabix_io_tabix_vcf ~/Development/healthplatform/data/gen/NA12878.vcf.gz chr1 10000 30000\r\n10056\tA\tAC\r\n10145\tAC\tA\r\n10176\tA\tAC\r\n10229\tAC\tA,AN\r\n10326\tT\tC\r\n10348\tCCCTA\tC,CCCTAA\r\n10388\tAC\tA,AN\r\n10395\tAC\tA\r\n10438\tAC\tA\r\n10468\tC\tG\r\n10615\tCCGCCGTTGCAAAGGCGCGCCG\tC\r\n10777\tC\tG\r\n10972\tT\tA\r\n14698\tC\tG\r\n14906\tA\tG\r\n14929\tA\tG\r\n15210\tT\tG\r\n15273\tA\tT\r\n16013\tC\tT\r\n16067\tT\tC\r\n16102\tT\tG\r\n16377\tT\tC\r\n17384\tG\tA\r\n17406\tG\tA\r\n20244\tG\tA\r\n20303\tG\tC\r\n20466\tC\tT\r\n28197\tA\tT\r\n28325\tGT\tG\r\n28353\tC\tT\r\n28375\tG\tA\r\n28562\tA\tG\r\n28588\tT\tTTTGG\r\n28862\tC\tA\r\n```\r\n\r\n\r\nLimitations:\r\n * the tbi index must be created with the distinct tabix tool (Heng Li)\r\n * if SAM with Tabix should be supported (actually we would recommend indexed BAM) one has to adapt ```_readTabixRecord``` to use the CIGAR to compute posEnd\r\n * to support all other tab-seperated chromosomal formats, e.g. BED, GFF, ..., one has to register bed.gz and gff.gz, ... as BGZF file extensions (which on the other hand forbids to use non-seekable standard gzip compressed files, they will be not recognized by their extension anymore)"},"comment":{"url":"https://api.github.com/repos/seqan/fx_tools/issues/comments/76631062","html_url":"https://github.com/seqan/fx_tools/pull/1#issuecomment-76631062","issue_url":"https://api.github.com/repos/seqan/fx_tools/issues/1","id":76631062,"user":{"login":"esiragusa","id":172085,"avatar_url":"https://avatars.githubusercontent.com/u/172085?v=3","gravatar_id":"","url":"https://api.github.com/users/esiragusa","html_url":"https://github.com/esiragusa","followers_url":"https://api.github.com/users/esiragusa/followers","following_url":"https://api.github.com/users/esiragusa/following{/other_user}","gists_url":"https://api.github.com/users/esiragusa/gists{/gist_id}","starred_url":"https://api.github.com/users/esiragusa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/esiragusa/subscriptions","organizations_url":"https://api.github.com/users/esiragusa/orgs","repos_url":"https://api.github.com/users/esiragusa/repos","events_url":"https://api.github.com/users/esiragusa/events{/privacy}","received_events_url":"https://api.github.com/users/esiragusa/received_events","type":"User","site_admin":false},"created_at":"2015-03-01T21:13:25Z","updated_at":"2015-03-01T21:13:25Z","body":"@weese thanks for the pr! ba3ea43d884f4db5b3b479e9657645d6223154 only fixes fx_bam_coverage, while 1cfc7f0e1e9f385e02790b0fd165b167953d9267 requires the tabix feature from develop, right?"}}