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cbirdlab / dDocentHPC

hard fork of dDocent, edited to run without interactive user input
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Config File issue #4

Closed jdselwyn closed 4 years ago

jdselwyn commented 4 years ago

This line in the config file: no freebayes -J --pooled-discrete (yes|no)

Needs to change to this: no freebayes -J --pooled-discrete (yes or no)

So the parsing of the genotyping properly goes to Individual genotyping not Pools with ploidy 2

cbird808 commented 4 years ago

I will update dDocentHPC.bash to accept either

cbird808 commented 4 years ago

I resolved this by dialing back the length of the search patterns for pulling the settings out of the config file. Changes have been pushed to github