In order to reduce the number of scripts the user chooses from, this PR adds an additional argument to the wrangler app, which controls the --fraccutoff argument. We have set the default value of this argument to the default value in MIPWrangler of 0.005. By doing so, we may remove the runMIPWranglerNoCutoffCurrent script and instead only have one script.
[^1]: We note that these scripts are also present within base_resources. Within this folder, there are also two scripts for running selective whole genome amplification (SWGA).
When running the
wranglerapp, the user is allowed to change the MIPWrangler script that is run to correct barcodes and cluster barcodes and MIPs together. Withinbin[^1] we have provided the user with two related scripts:(https://github.com/bailey-lab/MIPTools/blob/4d87dd6a3bcde9c372423563ae53f9c148639951/bin/runMIPWranglerCurrent.sh and https://github.com/bailey-lab/MIPTools/blob/4d87dd6a3bcde9c372423563ae53f9c148639951/bin/runMIPWranglerNoCutoffCurrent.sh). The difference between these two scripts is that one is designed to implement a population clustering fraction cutoff, whereas the other does not. This parameter is controlled via the--fraccutoffargument. For example, in the case where we don't want a cutoff, we have:https://github.com/bailey-lab/MIPTools/blob/4d87dd6a3bcde9c372423563ae53f9c148639951/bin/runMIPWranglerNoCutoffCurrent.sh#L10
In order to reduce the number of scripts the user chooses from, this PR adds an additional argument to the
wranglerapp, which controls the--fraccutoffargument. We have set the default value of this argument to the default value in MIPWrangler of0.005. By doing so, we may remove therunMIPWranglerNoCutoffCurrentscript and instead only have one script.[^1]: We note that these scripts are also present within
base_resources. Within this folder, there are also two scripts for running selective whole genome amplification (SWGA).