{"action":"created","issue":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/25","repository_url":"https://api.github.com/repos/Oshlack/STRetch","labels_url":"https://api.github.com/repos/Oshlack/STRetch/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/Oshlack/STRetch/issues/25/comments","events_url":"https://api.github.com/repos/Oshlack/STRetch/issues/25/events","html_url":"https://github.com/Oshlack/STRetch/issues/25","id":293346848,"number":25,"title":"Error in `Stage median_cov_target`","user":{"login":"ifiddes-10x","id":35242397,"avatar_url":"https://avatars3.githubusercontent.com/u/35242397?v=4","gravatar_id":"","url":"https://api.github.com/users/ifiddes-10x","html_url":"https://github.com/ifiddes-10x","followers_url":"https://api.github.com/users/ifiddes-10x/followers","following_url":"https://api.github.com/users/ifiddes-10x/following{/other_user}","gists_url":"https://api.github.com/users/ifiddes-10x/gists{/gist_id}","starred_url":"https://api.github.com/users/ifiddes-10x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ifiddes-10x/subscriptions","organizations_url":"https://api.github.com/users/ifiddes-10x/orgs","repos_url":"https://api.github.com/users/ifiddes-10x/repos","events_url":"https://api.github.com/users/ifiddes-10x/events{/privacy}","received_events_url":"https://api.github.com/users/ifiddes-10x/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2018-01-31T23:14:32Z","updated_at":"2018-02-06T04:04:38Z","closed_at":null,"author_association":"NONE","body":"I am trying to use the `STRetch_wgs_bam_pipeline.groovy` pipeline with a previously generated BAM against GRCh38, targeting a specific set of STRs I have identified in a BED file. After taking an hour to walk the BAM (why does it not use random access with the index?), it crashes with an error about the reference:\r\n\r\n```\r\n=========================== Stage median_cov_target (NA24143_longranger) ===========================\r\n2018/01/31 15:01:40 NA24143.bam\r\nchromosome: STR-A not found in NA24143.bam\r\nchromosome: STR-AAAAAC not found in NA24143.bam\r\nchromosome: STR-AAAAAG not found in NA24143.bam\r\nchromosome: STR-AAAAAT not found in NA24143.bam\r\nchromosome: STR-AAAAC not found in NA24143.bam\r\n\r\n... <removed lots of lines>\r\n\r\npanic: runtime error: index out of range\r\ngoroutine 1 [running]:\r\ngithub.com/brentp/goleft/covmed.BamInsertSizes(0xc42009a320, 0x186a0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0)\r\n        /home/brentp/go/src/github.com/brentp/goleft/covmed/main.go:106 +0x6c5\r\ngithub.com/brentp/goleft/covmed.Main()\r\n        /home/brentp/go/src/github.com/brentp/goleft/covmed/main.go:153 +0x5d6\r\nmain.main()\r\n        /home/brentp/go/src/github.com/brentp/goleft/main.go:65 +0x191\r\n\r\n\r\n```\r\n\r\nAm I misunderstanding how to use this pipeline? Do I need to be mapped against a special reference?"},"comment":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/comments/363304487","html_url":"https://github.com/Oshlack/STRetch/issues/25#issuecomment-363304487","issue_url":"https://api.github.com/repos/Oshlack/STRetch/issues/25","id":363304487,"user":{"login":"hdashnow","id":3794821,"avatar_url":"https://avatars2.githubusercontent.com/u/3794821?v=4","gravatar_id":"","url":"https://api.github.com/users/hdashnow","html_url":"https://github.com/hdashnow","followers_url":"https://api.github.com/users/hdashnow/followers","following_url":"https://api.github.com/users/hdashnow/following{/other_user}","gists_url":"https://api.github.com/users/hdashnow/gists{/gist_id}","starred_url":"https://api.github.com/users/hdashnow/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hdashnow/subscriptions","organizations_url":"https://api.github.com/users/hdashnow/orgs","repos_url":"https://api.github.com/users/hdashnow/repos","events_url":"https://api.github.com/users/hdashnow/events{/privacy}","received_events_url":"https://api.github.com/users/hdashnow/received_events","type":"User","site_admin":false},"created_at":"2018-02-06T04:04:38Z","updated_at":"2018-02-06T04:04:38Z","author_association":"COLLABORATOR","body":"Thanks, Ian. I've been able to replicate the error now. I'll let you know when I have a fix."}}
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