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added a few things to readme #26

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flashton2003
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hope you guys dont mind, just thought it might be useful?

no worries if not.

@alexjironkin
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We are keeping phenix.py as a single point of entry for the code. There are a bunch of other things that are set there and we want to keep it that way. We have kept ability to run run_snp_pipeline.py directly in the code purely for backwards compatibility. Otherwise, official running of all commands has to go through phenix.py <subcommand>

There is a typo in the (which I thought we fixed) that lists run_snp_pipeline.py instead of run_snp_pipeline.

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