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Add optional absolute threshold to trim_pwm - #196
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avantikalal merged 2 commits intoOct 7, 2026
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trim_pwm previously always treated trim_threshold as relative to the max per-position score, which is awkward for non-IC matrices such as PPMs. Add a relative flag (default True) so callers can opt into an absolute threshold while preserving backwards-compatible behavior. Fixes Genentech#125
avantikalal
approved these changes
Oct 7, 2026
avantikalal
approved these changes
Oct 7, 2026
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Summary
trim_pwm(trim_pwminconsistency #125): the function previously always treatedtrim_thresholdas relative to the max per-position score, which assumes an IC-style PWM and is awkward for more general matrices (e.g. PPMs).relative: bool = Trueso callers can request an absolute threshold (relative=False) while keeping the existing relative behavior as the default for backwards compatibility.API change
relative=True(default):trim_thresh = max(score) * trim_threshold(unchanged behavior)relative=False:trim_thresh = trim_threshold(absolute threshold on summed absolute weights per position)Test plan
pytest tests/test_interpret.py::test_trim_pwmpassesFixes #125