enable pep prefilter if available#117
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trishorts wants to merge 1 commit into
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I may close this PR b/c it only effects the standalone version.
In MetaMorpheus, we are slowly moving on from q-value filter and relying more and more on PEP. This PR, tells FlashLFQ to prefilter on PEP and PEP Q-value if those parameters are specified. If they are not, the default reverts to q-value and q-value notch.