Reference HGVS without reference base leads to wrong coordinates and reference allele

[davmlaw]

The current regex treats the last digit as a ref digit, ie it uses it to multiply "N" that many times. This makes the coordinate wrong as the last digit is cut off, eg:

In [6]: HGVSName("NC_000017.11:g.50199235=")                                                                                                                               
Out[6]: HGVSName('NC_000017.11:g.5019923NNNNN=')

In [7]: HGVSName("NM_018090.5:c.462=")                                                                                                                                     
Out[7]: HGVSName('NM_018090.5:c.46NN=')

Unit test test_hgvs_names.py

# Copy pasted from BRCA1:c.101A= test with "A" removed

    ('BRCA1:c.101=', True,
     {
         'gene': 'BRCA1',
         'kind': 'c',
         'cdna_start': CDNACoord(101),
         'cdna_end': CDNACoord(101),
         'ref_allele': '',
         'alt_allele': '',
         'mutation_type': '=',
     }),

# Copy pasted from BRCA1:g.101A= test with "A" removed

    ('BRCA1:g.101=', True,
     {
         'gene': 'BRCA1',
         'kind': 'g',
         'start': 101,
         'end': 101,
         'ref_allele': '',
         'alt_allele': '',
         'mutation_type': '=',
     }),

Currently fails with:

AssertionError: CDNACoord(10, 0) != CDNACoord(101, 0)

Fix is to add a new regex just above the existing "No change" regexes, ie in HGVSRegex:

CDNA_ALLELE = [
    CDNA_START + EQUAL, 
    # old regexes
]

GENOMIC_ALLELE = [
    COORD_START + EQUAL,
    # old regexes
]

I am not sure whether the protein HGVS is affected, and if need to specify the ref ie whether "p.1000=" is valid or not