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comparison build_matrix.R @ 15:65739ddd00be draft

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author greg
date Thu, 10 Aug 2017 14:23:32 -0400
parents c59cbd44dcff
children 79acab9c6524
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14:3b3bf5196bbe 15:65739ddd00be
3 suppressPackageStartupMessages(library("optparse")) 3 suppressPackageStartupMessages(library("optparse"))
4 4
5 option_list <- list( 5 option_list <- list(
6 make_option(c("-i", "--input"), action="store", dest="input", help="Input .bed.gz file produced by prepMat"), 6 make_option(c("-i", "--input"), action="store", dest="input", help="Input .bed.gz file produced by prepMat"),
7 make_option(c("-o", "--output"), action="store", dest="output", help="Output file"), 7 make_option(c("-o", "--output"), action="store", dest="output", help="Output file"),
8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory"),
8 ) 9 )
9 10
10 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
11 args <- parse_args(parser, positional_arguments=TRUE) 12 args <- parse_args(parser, positional_arguments=TRUE)
12 opt <- args$options 13 opt <- args$options