SV plugin updates

[nakib103]

No description provided.

[mluypaert]

Is CADD really the only plugin we want to run for Structural variants? Should all others be disabled (as this code does)?

[nakib103]

the only other candidate is Phenotype, but we will have separate data store for it soon.

[mluypaert]

@nakib103 As the phenotype store is still in design, I'd say we should keep the current phenotype plugin enabled until we have access to the new data.

[nakib103]

Phenotype plugin data (the GFF3s) has the phenotype for structural variants. But I don't think anyone ever tested/worked on the plugin to see if it works with that data (you might get lots of Pheno against short variants getting attached to the SVs).
But if you already have tested and have good hunch about it I can add the plugin.

[mluypaert]

Suggested change

	plugin_files = []
	if structural_variant:
	sv = os.path.join(plugin_data_dir, "CADD_prescored_variants.tsv.gz")
	plugin_files = [sv]
	else:
	if species == "sus_scrofa":
	snv = os.path.join(plugin_data_dir, "ALL_pCADD-PHRED-scores.tsv.gz")
	plugin_files = [snv]
	else:
	snv = os.path.join(
	plugin_data_dir, f"CADD_{assembly}_1.7_whole_genome_SNVs.tsv.gz"
	)
	indels = os.path.join(plugin_data_dir, f"CADD_{assembly}_1.7_InDels.tsv.gz")
	plugin_files = [snv, indels]
	if len(plugin_files) > 0:
	check_plugin_files(plugin, plugin_files)
	return f"CADD,{','.join(plugin_files)}"
	else:
	return ''

[mluypaert]

The suggested change here should span lines 325 - 344, for some reason it doesn't seem to get the formatting right (It's not just adding 21 lines but rather replacing the 19 existing ones with the 21 above)

[nakib103]

I have added the suggestion with slight modification.

[mluypaert]

Why still repeating the check_plugin_files function-calling and the return value formatting logic? My suggestion was mostly about not repeating that logic (it only calls check_plugin_files and formats and returns the CLI arg on one line by making use of the plugin_files array).

[nakib103]

ah that might be right, it was hard reading with wrapped lines. I kept it this way for better readability.