Wrong variant mapping result for identity variant

[icebert]

For identity variant, the replace reference function in variant mapper only changes the ref of edit, causing the ref and alt discordant.

Example code:

import hgvs.parser
import hgvs.assemblymapper
import hgvs.dataproviders.uta

hp = hgvs.parser.Parser()

hdp = hgvs.dataproviders.uta.connect()

am = hgvs.assemblymapper.AssemblyMapper(hdp, normalize=False)


var = 'NM_001292004.1:c.376='

var_c = hp.parse_hgvs_variant(var)

var_g = am.c_to_g(var_c)

str(var_g)

NC_000005.10:g.74715659delins

The correct mapping result should be NC_000005.10:g.74715659= instead of NC_000005.10:g.74715659delins.

[icebert]

I ignored the case that the referecne sequence of transcripts and genome may be different. When variants occured on such sites, the mapped result of ident var may not be ident var. I will make a new pull request.