"""
Completeness-filtered absence analysis (produces fig_completeness_absence.png + completeness_absence.csv).
Filters the feature matrix to high-quality genomes (CheckM completeness >=90%, contamination <=5%; n=2,018),
then tabulates methanogenesis / Wood-Ljungdahl / reverse-gyrase carriage among halophiles, split by
Halobacteria-clade vs non-Halobacteria measured-salt halophiles. Confirms the absence in Halobacteria
halophiles is real (complete genomes), not a sequencing artefact.
Inputs: feature_matrix.csv, trait_matrix.csv, and the 12 per-marker HMMER .domtbl files.
"""