Open nevrome opened 4 years ago
@TCLamnidis
unset _janno_files
thing - could you elaborate? Isn't it necessary to create an empty array when I want to append to it?@AyGhal
.pedind
file is indeed necessary due to column order and we can consider this question raised by He above as solved, ja?--keep-allele-order
thing? I'm sure Elina would not mind commenting this. I even believe she has a Github account, but I don't know the name.@nevrome
Yes, the pedind file is necessary because of the location(column) of population label in plink & eigensoft.
--keep-allele-order option was added.
Yes. There is no need to create an empty array before appending to it. See below:
$ echo ${test[@]} # test is empty
$ test+=("banana") # append "banana"
$ echo ${test[@]}
banana
$ test+=("banana") # append again
$ echo ${test[@]}
banana banana
$ test+=("banana") # and again
$ echo ${test[@]}
banana banana banana
$ unset test # unset to make empty again
$ test+=("banana") # append again
$ echo ${test[@]}
banana
The current code isn't buggy or anything, so maybe this is just aesthetics/me being stuck in my ways, but the the syntax highlighting on my text editor did get tripped up by it.
@esalmela could you comment on the --keep-allele-order? I cannot remember the outcome of our discussions on the plink merging and converting to Eigenstrat.
He
@TCLamnidis
[x] No check for too many arguments. Could lead to odd results that "worked" when a user provides multiple input files for eg.
[x] Log folder could get messy if someone submits jobs in a loop, as multiple jobs will have same time stamp. could cause issues when jobs are sbatched. Perhaps add a hash to the end of the folder? Or maybe deter people from looping with a check for this logdir existing and an error?
[x] _print_packages also prints commented out lines or comments in the lines. Bug or feature?
[ ] poseidon_merge
unset _janno_files
. the current fomrulation will trip text editors into thinking _janno_files is a function definition. (minor thing)