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rwdavies / STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
GNU General Public License v3.0
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generateInputOnly doesn't work as expected #1

Closed hliang closed 7 years ago

hliang commented 7 years ago

It says: #' @param generateInputOnly Whether to just generate input data then quit, but when I ran stitch with generateInputOnly=TRUE, it continued and finished all the following imputation steps.

I had to make it stop by inserting the these lines after generate_or_refactor_input(...) in file STITCH/R/functions.R.

## quit after input .RDate files are generated
if(generateInputOnly) {
  return(NULL)
}

BTW, I was running version 1.2.4.

rwdavies commented 7 years ago

Thanks, you're right. I must have broken that while re-factoring the input generation, and didn't have a test to check that it properly stopped at that point. I'll add a patch and test in the upcoming days

rwdavies commented 7 years ago

This is fixed now with v1.3.1