Cava

support transcripts in MANE 1.0 (unit tests included) for genes without UTR.(FOXL3)
Moved this version back to Python 3.6 (last one was python 3.7)
FIx bugs for variants around edges.
- indels at edges when no UTR present.
- indels at edge of start codon.
Removed overcalling of variant function past the edges of the transcript range (as per HGVS).
Support larger deletions partially overlapping with splice sites and intron/exon junctions.
Support larger deletions spanning exons (though it calls it p.?, but will call the cDNA))
Include proper (though conservative) support for selenocysteine genes.
Added comments.
Included MANE 1.0 in unit test directory.

As a side note I did notice one omission in CAVA. It does not call Start gains in the 5'UTR. This was not fixed.

Also, in-frame-deletions in repeated elements was off by one in cDNA position. This bug has been fixed.

Updating to allow for earlier version of python (3.6)

New Features:
CAVA_HGVSg added with support for ins,del,dup, repeats,
CAVA_HGVSc now supports repeats.
Support gVCF <NON_REF> or <*> alleles (they are just put back in the output)
Clean results from previous CAVA annotation runs from INFO field before adding new ones.
added "build" options to config file (defaults to GRCh38)

Revert back to trust the downloads

Only affects liftover from MANE DBs

Uses HTTPS instead of FTP for MAN downloads