broadinstitute / adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.
MIT License
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Consider changing default objective function to `maximize-activity` #38

Closed haydenm closed 1 year ago

haydenm commented 3 years ago

When no objective function is set, it defaults to minimize-guides: https://github.com/broadinstitute/adapt/blob/02bf2b9667a313c9784e1a8a2053cbe2d338b99d/bin/design.py#L754

The reason for this is that minimize-guides can work naturally without an activity model specified (i.e., just using -gm). However, we normally recommend using the maximize-activity objective and most of our paper used this objective, so it might make sense to make it the default. There are a few options if this were the default:

haydenm commented 1 year ago

This issue is resolved by #70.

70 takes the second option in the issue description ("If no activity model is specified with this objective, immediately exit and tell the user to give one or set --use-simple-binary-activity-prediction").