updateBimFam = function(hub) {
# create symlinks for bim and fam files
shift0BedFile = paste(hub$bedStem, "_shift_0000.bed", sep="")
shift0FamFile = paste(hub$bedStem, "_shift_0000.fam", sep="")
shift0BimFile = paste(hub$bedStem, "_shift_0000.bim", sep="")
file.remove(c(shift0FamFile, shift0FamFile, shift0BimFile))
file.remove(hub$shiftFilesBim)
file.remove(hub$shiftFilesFam)
# Linking bim and fam files
currentDir = getwd()
tryCatch({
setwd(hub$wDir)
bedBase = basename(hub$bedPath)
famBase = basename(hub$famPath)
bimBase = basename(hub$bimPath)
shiftBaseBed = basename(hub$shiftFilesBed)
shiftBaseFam = basename(hub$shiftFilesFam)
shiftBaseBim = basename(hub$shiftFilesBim)
shift0BedBase = basename(shift0BedFile)
shift0BimBase = basename(shift0BimFile)
shift0FamBase = basename(shift0FamFile)
file.symlink(bedBase, shift0BedBase)
file.symlink(famBase, shift0FamBase)
file.symlink(bimBase, shift0BimBase)
file.symlink(famBase, shiftBaseFam)
file.symlink(bimBase, shiftBaseBim)
},
error = function(e) {
message("Error in updateBimFam!")
return(invisible(FALSE))
},
finally = {
setwd(currentDir)
})
invisible(TRUE)
}
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