{"action":"opened","issue":{"url":"https://api.github.com/repos/mathieu-lemire/celluloid_0.11_tutorial/issues/1","repository_url":"https://api.github.com/repos/mathieu-lemire/celluloid_0.11_tutorial","labels_url":"https://api.github.com/repos/mathieu-lemire/celluloid_0.11_tutorial/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/mathieu-lemire/celluloid_0.11_tutorial/issues/1/comments","events_url":"https://api.github.com/repos/mathieu-lemire/celluloid_0.11_tutorial/issues/1/events","html_url":"https://github.com/mathieu-lemire/celluloid_0.11_tutorial/issues/1","id":184082849,"number":1,"title":"fist issue! Error in sample.int","user":{"login":"RichardCorbett","id":9285915,"avatar_url":"https://avatars.githubusercontent.com/u/9285915?v=3","gravatar_id":"","url":"https://api.github.com/users/RichardCorbett","html_url":"https://github.com/RichardCorbett","followers_url":"https://api.github.com/users/RichardCorbett/followers","following_url":"https://api.github.com/users/RichardCorbett/following{/other_user}","gists_url":"https://api.github.com/users/RichardCorbett/gists{/gist_id}","starred_url":"https://api.github.com/users/RichardCorbett/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RichardCorbett/subscriptions","organizations_url":"https://api.github.com/users/RichardCorbett/orgs","repos_url":"https://api.github.com/users/RichardCorbett/repos","events_url":"https://api.github.com/users/RichardCorbett/events{/privacy}","received_events_url":"https://api.github.com/users/RichardCorbett/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-19T21:47:23Z","updated_at":"2016-10-19T21:47:23Z","closed_at":null,"body":"Hi there,\r\nI thought I'd give your code a try after seeing the paper.\r\n\r\nCommand:\r\n`R-3.3.0/bin/Rscript pipeline.r ../../HMMCopy/tum_reads.wig ../../HMMCopy/norm_reads.wig ../../HMMCopy/gc.wig ../../HMMCopy/GRCh37-lite_125bp.map.bw.wig ../hetCounts.txt colo829\r\n`\r\nand after the packes are all loaded I get an error:\r\n`Loading required package: XML\r\nIdentifying and ignoring outlier read counts...Error in sample.int(length(x), size, replace, prob) : \r\n  invalid first argument\r\nCalls: gcCorrect -> gcCorrect.normal -> sample -> sample.int\r\n`\r\n\r\nHere are the first lines of each of my wig files:\r\ntum_reads.wig\r\n> fixedStep chrom=1 start=1 step=1000 span=1000\r\n> 0\r\n> 0\r\n\r\nnorm_reads.wig\r\n> fixedStep chrom=1 start=1 step=1000 span=1000\r\n> 0\r\n> 0\r\n\r\ngc.wig\r\n> fixedStep chrom=1 start=1 step=1000 span=1000\r\n> -1\r\n> -1\r\n\r\nGRCh37-lite_125bp.map.bw.wig\r\n> fixedStep chrom=1 start=1 step=1000 span=1000\r\n> 0\r\n> 0\r\n\r\nhetCounts.txt\r\n> CHR POS REF_COUNT VAR_COUNT\r\n> 10 60637 73 46\r\n> 10 60684 73 43\r\n\r\nThe files listed above that have lines with 0s and -1s do have proper values once you get in to the meat of the file.  Do you have any ideas of things to check?\r\n"}}
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