ClinVar variation != "single nucleotide variant" in ADDB 2019+

[krassowski]

While addressing some automated code complexity warnings over on #168 I noticed that the check for variation_type for ClinVar is correctly executed but there is no following continue instruction that would lead to filtering out non-SNV variants:

ActiveDriverDB/website/imports/mutations/clinvar.py

Lines 257 to 261 in 5e9d2c3

	variation_type = variation.attrib['Type']
	if variation_type != 'single nucleotide variant':
	if variation_type not in skipped_variation_types:
	print(f'Skipping variation type: {variation_type}')
	skipped_variation_types.add(variation_type)

However, it appears likely that they are not included either way, because there is another filter earlier in the pipeline, when the mutations are mapped with annovar:

ActiveDriverDB/website/data/mutations/annotate_clinvar.sh

Line 10 in cc4873a

cat clinvar_annotated.hg19_multianno.txt | awk -F '\t' "BEGIN{print \"$(head clinvar_annotated.hg19_multianno.txt -n 1)\";};\$9 ~ /nonsynonymous SNV/" | gzip > clinvar_muts_annotated.txt.gz

It would be good to investigate this further. For now, I will add a TODO note in the code to highlight this issue.