Dave Lawrence comments

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                                            Dave Lawrence

GenotypeGVCFs: Add ability to convert current (0/0) genotype format to standard (./.) format

If you want efficiency - output a new file format, don't output a file labelled VCF that violates the specs

GenotypeGVCFs: Add ability to convert current (0/0) genotype format to standard (./.) format

[Release 4.6.0.0](https://github.com/broadinstitute/gatk/releases/tag/4.6.0.0) > By overwhelming popular demand, we've switched back to using the standard ./. representation for no-calls in GenotypeGVCFs and GenomicsDB instead of 0/0 with DP=0

Crash with single GT allele value - UnicodeDecodeError: 'ascii' codec can't decode byte 0x81 in position 1: ordinal not in range(128)

Thanks - will do that as a workaround. I usually use the specific methods (which work fine), in this case I wanted to store all format fields in JSON

Validation - refactor to be able to retrieve all errors rather than throw exception on 1st

I posted this in HGVS slack but it disappeared after 90 days so re-raising here

Normalizer constructor doesn't pass the `validate` param to the VariantMapper constructor

Fixed w/Pull request

Modify parser to include common errors to provide better error messages than "syntax error"

I am happy to do the work and make a pull request, just raising the issue for discussion

Modify parser to include common errors to provide better error messages than "syntax error"

Potentually related to #367

fix: update gene symbol when it is `None` and `AssemblyMapper` normalizer

Hi, thanks for the pull request, here are some comments on the change: 1. **_update_gene_symbol** The existing code: ``` if not symbol: ``` Already handles symbol being None - I...

fix: update gene symbol when it is `None` and `AssemblyMapper` normalizer

@markgene - thanks for your contribution, I have taken your change, removed the gene parts, and added a unit test - submitted as a new pull request: https://github.com/biocommons/hgvs/pull/746

bindfields.js expects 'data-value' to be JSON but widgets.py doesn't always encode it

Sorry, I use Django autocomplete light now, so can't easily test this. Feel free to close if you think it's fixed.