{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/50","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/50/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/50/events","html_url":"https://github.com/arq5x/lumpy-sv/pull/50","id":53551893,"number":50,"title":"Read group awareness","user":{"login":"cc2qe","id":3903682,"avatar_url":"https://avatars.githubusercontent.com/u/3903682?v=3","gravatar_id":"","url":"https://api.github.com/users/cc2qe","html_url":"https://github.com/cc2qe","followers_url":"https://api.github.com/users/cc2qe/followers","following_url":"https://api.github.com/users/cc2qe/following{/other_user}","gists_url":"https://api.github.com/users/cc2qe/gists{/gist_id}","starred_url":"https://api.github.com/users/cc2qe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cc2qe/subscriptions","organizations_url":"https://api.github.com/users/cc2qe/orgs","repos_url":"https://api.github.com/users/cc2qe/repos","events_url":"https://api.github.com/users/cc2qe/events{/privacy}","received_events_url":"https://api.github.com/users/cc2qe/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-01-06T19:22:20Z","updated_at":"2015-01-07T00:58:14Z","closed_at":"2015-01-07T00:58:06Z","pull_request":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/pulls/50","html_url":"https://github.com/arq5x/lumpy-sv/pull/50","diff_url":"https://github.com/arq5x/lumpy-sv/pull/50.diff","patch_url":"https://github.com/arq5x/lumpy-sv/pull/50.patch"},"body":"These modifications make LUMPY read group aware, simplifying integration into the SpeedSeq pipeline. Mainly, allows us to merge all splitters and discordant files from different libraries on a per-sample basis prior to running LUMPY.\r\n\r\nUsers may now specify one or more read groups to consider in the -pe and -sr command line arguments of LUMPY. The intended usage is for each -pe blob to process a single library (potentially with multiple read groups), drawing from the proper insert size distribution. If there are multiple libraries in a single BAM file, then the -pe blob can be called multiple times, each with read groups from the unique library while repeating the BAM file. If the \"read_group\" parameter is omitted, LUMPY behaves exactly as it did before: considering all read_groups in the BAM file.\r\n\r\nExample:\r\n```\r\nlumpy \\\r\n    -mw 4 \\\r\n    -tt 0 \\\r\n    -pe bam_file:A-CUHS-CU000063.merged.discordants.bam,histo_file:2893594432.x4.histo,mean:230.216068583,stdev:27.0862036746,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:100,min_mapping_threshold:20,read_group:2893594432 \\\r\n    -pe bam_file:A-CUHS-CU000063.merged.discordants.bam,histo_file:2893594429.x4.histo,mean:473.270630769,stdev:100.489159512,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:110,min_mapping_threshold:20,read_group:2893594429 \\\r\n    -pe bam_file:A-CUHS-CU000063.merged.discordants.bam,histo_file:2893594379.x4.histo,mean:330.345984874,stdev:37.3689979312,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:120,min_mapping_threshold:20,read_group:2893594379 \\\r\n    -sr bam_file:A-CUHS-CU000063.merged.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:101,min_clip:20 \\\r\n    > A-CUHS-CU000063.multi.lumpy\r\n```\r\n\r\nBy my testing, these modifications do not affect speed:\r\n 8d7eb49ce18496217bf2f7d088c9337cb6f88f68: 3028.69 sec\r\n588046880592ebc4aaf5cf299cf6956f8c699a59: 3034.13 sec"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/68962658","html_url":"https://github.com/arq5x/lumpy-sv/pull/50#issuecomment-68962658","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/50","id":68962658,"user":{"login":"ryanlayer","id":607057,"avatar_url":"https://avatars.githubusercontent.com/u/607057?v=3","gravatar_id":"","url":"https://api.github.com/users/ryanlayer","html_url":"https://github.com/ryanlayer","followers_url":"https://api.github.com/users/ryanlayer/followers","following_url":"https://api.github.com/users/ryanlayer/following{/other_user}","gists_url":"https://api.github.com/users/ryanlayer/gists{/gist_id}","starred_url":"https://api.github.com/users/ryanlayer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryanlayer/subscriptions","organizations_url":"https://api.github.com/users/ryanlayer/orgs","repos_url":"https://api.github.com/users/ryanlayer/repos","events_url":"https://api.github.com/users/ryanlayer/events{/privacy}","received_events_url":"https://api.github.com/users/ryanlayer/received_events","type":"User","site_admin":false},"created_at":"2015-01-07T00:58:14Z","updated_at":"2015-01-07T00:58:14Z","body":"This looks great.  Even fixed some of my typos! Thanks Colby."}}