Minimum reportable repeat score -s is parsed but never applied

[domen13]

The -s/--score flag is documented as "Minimum reportable repeat score" and is correctly parsed into Settings::min_score (confirmed via the .bed.settings JSON output, which correctly reflects whatever value is passed). However, the reported repeats in the output are completely unaffected by this value. I get identical output whether I pass --score -10000, --score 0, or --score 10000.

Reproduction

ultra --bed --score -10000 -o out_low.bed  examples/example_3.fa
ultra --bed --score 10000 -o out_high.bed examples/example_3.fa
diff out_low.bed out_high.bed   # no difference

Root cause

ULTRA/src/ultra.cpp

Line 485 in a3a5ba6

scoreThreshold = settings->min_score;

scoreThreshold is assigned here but is never read anywhere else in the codebase.