suppressPackageStartupMessages(library(argparse))
suppressPackageStartupMessages(library(epiRepeatR))
ap <- ArgumentParser()
ap$add_argument("-i", "--in", action="store", dest="input", help="Input file (RDS) containing a RepeatEpigenomeCollection object as R dataset.")
ap$add_argument("-o", "--out", action="store", dest="output", help="Output directory")
ap$add_argument("-c", "--config", action="store", help="Config file (json)")
cmdArgs <- ap$parse_args() #problem: too long of a command line
logger.cmd.args(cmdArgs)
loadConfig(cmdArgs$config)
if (is.element("debug", names(epiRepeatR:::.config)) && epiRepeatR:::.config$debug){
saveRDS(cmdArgs, file.path(cmdArgs$output, "cmdargs.rds"))
}
rec <- readRDS(cmdArgs$input)
epiRepeatR:::createRepPlot_markTree(
rec, cmdArgs$output, leafColorMethod=getConfigElement("plotRepTree.leafColorMethod"),
dendroMethod=getConfigElement("plotRepTree.dendroMethod"), normChipMethod=getConfigElement("plotRepTree.normEnrich"),
minReads=getConfigElement("plotRepTree.meth.minReads"), minCpGs=getConfigElement("plotRepTree.meth.minCpGs"), minCpGcov=getConfigElement("meth.minCpGcov")
)
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