Summary:

In this MR we are adding support to create correct hgvs_p names, for variants that impact Selenocysteine positions.

Previously they would yield p.?, however now it is possible to create names like NP_065184.2:p.Sec462Arg, or NP_065184.2:p.U127del

Details:

1. Implemented selenocysteine auto-detection in RefTranscriptData.init:

• After getting the protein accession, fetches the reference protein sequence

• Checks if it contains 'U' (selenocysteine)

• If found, re-translates using TranslationTable.selenocysteine

• Stores the actual translation table used in self.translation_table

2. Updated VariantMapper.c_to_p to use the detected translation table:

• Passes reference_data.translation_table to AltSeqBuilder so variant sequences use the correct table

Unfortunately also needed to address linting in the files, since I could not commit otherwise.