Score Compounds

This module performs ranking of compound variants.

[!WARNING] Ranking of compound variants is only done for the first family in the VCF.

During the ranking of these compounds the rank score might be modified in place. See genmod/score_variants/compound_scorer.py:L248.

Rankscore Capping

Since the rank scores are modified in place in this module, there's a risk that the modified rank score might fall outside the valid range of normalization bounds (MIN, MAX) that was established in the score_variants module.

This applies to variants belonging to the lower range of rank scores.

When this happens, the modified rank score is capped to (MIN, ) if it's of RankScore type or (0, 1) if it's of RankScoreNormalized type.

In previous Genmod versions there were no such capping rule in effect. Earlier ranked variants from compounds module might show lower rank scores compared to this implementation.