Fix SV warnings for short variants in region format

[nuno-agostinho]

Fixes #1617: when inputting short variants in region format, VEP prints a warning message:

WARNING: line 1 skipped (12:9079672-9079672:C): C type is not supported

Also, unknown SV types in region format are incorrectly returned with no warning.

Changelog

This PR does the following:

• Remove the nonsense warning for short variants in region format
• Throw warning (and do not return output) when using SVs whose type is not supported

Testing

Ensure that running VEP with the following variants works without warnings¹:

12:9079672-9079672:C
12:9079672-9079672:DUP
12:9079672-9079672:INS:ME
12:9079672-9079672:INS:ME:LINE1

Ensure that running VEP with the following variants does not print output (only warnings):

12:9079672-9079672:RANDOM
12:9079672-9079672:DELTEST

Footnotes

1. The last two examples require https://github.com/Ensembl/ensembl-variation/pull/1071 ↩

[olaaustine]

LGTM, first test returns output and no warnings, second returns no output and warnings. Same result with the SNP

[olaaustine]

Merged into main and release/112