Incorrect HGVS to VCF conversion for some genomic indels

[davmlaw]

Hi, genomic indels are often wrong because get_coords() adjustment of start/end is only done for indels if self.kind == 'c'

Testing against examples from the ClinGen allele registry:

http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000492.3%3Ac.1155_1156dupTA

    'NM_000492.3:c.1155_1156dupTA' # correct resolves to ('chr7', 117182104, 'A', 'AAT')
    # Same as above but without optional trailing base - issue #32
    'NM_000492.3:c.1155_1156dup' # Error - resolves to ('chr7', 117182107, 'A', 'A')
    # Genomic coordinate of above
    "chr7:g.117182108_117182109dup" # Error - resolves to ('7', 117182109, 'A', 'A')

    # Genomic coordinate of above but shifted with optional base suffix
    "chr7:g.117182105_117182106dupAT" # Error - resolves to ('7', 117182106, 'T', 'T')

I would do a pull request but I've been working with existing pull request #25 and it doesn't look like this project is being updated anymore. If you merge #25 please ping this issue and I'll make a pull request.

Fixes are to remove test for if self.kind == 'c': in get_coords()

I've patched my fork: https://github.com/sacgf/hgvs

[davmlaw]

Sorry it appears that some of my bugs have already been reported in #32