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Main has two try/except statements to allow for one exit point when failed - returning 2, and returning 0 on success. The config will now add contamination if not == 0
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Main has two try/except statements to allow for one exit point when
failed - returning 2, and returning 0 on success. The config will now
add contamination if not == 0
The only thing to check is to see if the argument parser is handling the arguments that are 'files' correctly. I may need the BAMs to test because it looks like the argparser is collecting the 'files' as file objects if you look at the config file, and I don't know how that will run with controlFreeq.
But otherwise it works from a log and config file generating standpoint.