Dave Lawrence comments

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                                            Dave Lawrence

jQuery Imports and accessing $.fn.select2

I had the same issue on Django 2.1, I think this is the same as #1053 Removing just the line from select2 widgets.py: ``` 'admin/js/vendor/jquery/jquery%s.js' % extra, ``` Fixes everything.

Biopython 1.79 Fails to parse new Uniprot file in SwissProt text format

Confirmed that this is still broken with current UniProt file on latest PyPI release and fixed in GitHub master

Can't install from source

Completely separate, but I had some install issues, which I've fixed and will document here in case anyone wants workarounds HTSLib - I got ```missing config.sub config.guess``` I found this...

Accessing Variant num_called property causes segmentation fault

Hi just to note this still occurs with version '0.30.18' (latest PyPi release) Pisces 5.2.11.63 VCFs (From Illumina TSO500) define GT in the header but it's not in the FORMAT...

Add support for the telomer-to-telomer assembly (T2T)

I've added T2T in [cdot](https://github.com/SACGF/cdot), here's where I got the transcripts: RefSeq transcripts: https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_03/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz Ensembl transcripts: https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_06/Homo_sapiens-GCA_009914755.4-2022_06-genes.gff3.gz https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_07/Homo_sapiens-GCA_009914755.4-2022_07-genes.gff3.gz

Make the HGVS parser as a separate package

This is basically a dupe of #199 - requesting a reduction of dependencies

Provide utility to generate transcript variants from HGVS-ish expressions with gene names

Hi, I've had to implement this, and after putting it in front of medical scientists, I found the "generate everything" was slow and not that helpful to them. What they...

Index Error for variant using am37.c_to_g()

**Validation problem?** Other tools seem to think this is an error, so perhaps it's a validation problem: ClinGen allele registry: dies with "intronic position inside exon" Variant Validator: ExonBoundaryError: Position...

implement linters / static analyzers

@reece is this done enough now to close this issue?

protein change annotation difference between hgvs and vep

Hi - HGVS correctly handles alignment gaps here. The bug is with Ensembl VEP - I have already [raised this issue with them](https://github.com/Ensembl/ensembl-vep/issues/1053)