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Added an argument mode manager and a demonstration of how it might be used in HaplotypeCaller --dragen-mode #7745
Added an argument mode manager and a demonstration of how it might be used in HaplotypeCaller --dragen-mode #7745
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Add a comment documenting when in the arg parsing process this method needs to be invoked (eg., after args have already been parsed in
customCommandLineValidation()
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done
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How do we avoid setting these arg values if we're not in the specified mode?
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This method should only be called if the tool has already determined that it must be set. I added a note about it.
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Would it be a good idea for
setArgValues()
itself to check whether the provided mode is activated, and proceed with setting the args only if it's active? Or is an external check on the mode like you have here preferable? Either way, we don't need to address in this PR.There was a problem hiding this comment.
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This is a good point. I think ultimately the right place for this utility to live is in barclay and consequently this should maybe be automatic? This is a stopgap that helps handle the proliferation of messy argument mode switches in our tools for now.