Raise error if input file is incomplete

[youngchanpark]

data.table outputs a warning message if it tries to read an incomplete file:

Warning message:
In data.table::fread(filepath, select = c(chr, pos, a1, a2, pval,  :
  Discarded single-line footer: <<6     6:28098445      28098445        T       G       0.0478  0.0051  0.0424  0.0527  -0.0115 0.0>>

In this particular case, I was trying to read a file which was still copying. So what data.table did was to just remove the incomplete line and saved the remaining content. I think an error would be more appropriate than a warning message.

[agilly]

This is a behaviour of fread which cannot easily be circumvented as far as I know. What could be done is to check after loading that all autosomes are present, and then error out unless an option --ignore-filechecks is present.