updateShiftFiles = function(hub) {
hub$shiftFilesBed = sort(Sys.glob(sprintf("%s*.bed", hub$shiftStemCommon)))
if(length(hub$shiftFilesBed) > 0) {
hub$shiftFilesStem = getstem(hub$shiftFilesBed)
hub$shiftFilesBim = paste(hub$shiftFilesStem, ".bim", sep="")
hub$shiftFilesFam = paste(hub$shiftFilesStem, ".fam", sep="")
}
if(!all(file.exists(hub$shiftFilesBim) || !all(file.exists(hub$shiftFilesFam)))) {
updateBimFam(hub)
}
# get shift numbers
hub$nShiftStrs = getNshiftStr(hub$shiftFilesStem)
hub$nShift = as.integer(hub$nShiftStrs)
hub$nTotalShifts = length(hub$shiftFilesStem)
if(dbgtrigger()) {
message("List of shifted bed files:")
print(hub$shiftFilesBed)
}
invisible(NULL)
}
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