Compounds only scores first family in VCF

[fellen31]

Genmod compounds only scores the first family in the VCF. This is not clear from the documentation and only from TODO statements in the code.

This would be nice to fix, or at least document, since other parts of genmod works with multiple families.

genmod/genmod/score_variants/compound_scorer.py

Lines 185 to 190 in e45ff43

	#TODO check if correct family id
	# Right now we assume that there is only one family in the vcf
	family_id = family_rank_score[0]
	rank_score = float(family_rank_score[-1])
	rank_scores[rank_score_type][variant_id] = rank_score

genmod/genmod/score_variants/compound_scorer.py

Lines 228 to 235 in e45ff43

	#TODO Only checks first family now
	family_compound_entry = raw_compounds.split(',')[0]
	splitted_entry = family_compound_entry.split(':')
	compound_family_id = splitted_entry[0]
	compound_list = splitted_entry[-1].split('|')
	logger.debug("Checking compounds for family {0}".format(
	compound_family_id))

[dnil]

It popped up in linting as well! 😅 Maybe not bug-bug, especially since we always run it one family at the time, but definitely worth fixing.

[fellen31]

No maybe not bug, so I removed the label. But in Nallo we ran it with multiple families at the time before I discovered this.