generate_stat_report tries to parse iguide_dir from other arguments

cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

https://iguide.readthedocs.io/en/latest/

GNU General Public License v3.0

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generate_stat_report tries to parse iguide_dir from other arguments #46

Closed ressy closed 5 years ago

ressy commented 5 years ago

I have a directory path with "...-iguide" in my analysis, and when generate_stat_report.R greps for "-i" in its argument list it finds that path and tries to figure out the iguide_dir setting from it. Anchoring those two greps like "^-i" so it has to start at the beginning seems like a simple fix though.

ressy commented 5 years ago

Maybe like this? https://github.com/cnobles/iGUIDE/compare/master...ressy:generate-stat-report-args

cnobles commented 5 years ago

Fixed in #52 by converting over to argparser. This is consistent with the other scripts.