Dave Lawrence

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

2

If a VCF has a single GT value, cyvcf2 crashes out with: ```UnicodeDecodeError: 'ascii' codec can't decode byte 0x81 in position 1: ordinal not in range(128)``` [VCF spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf) says >...

The [GFF format](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) has a "phase" column on CDS features (values 0,1,2) which alter the reading frame of exons and the translation to amino acids. The UTA/DataProvider transcript annotation format...

Exon boundary / intron validation - need for genome build specific validation?

5

Biocommons HGVS currently performs no validation on whether an intronic coordinate is valid or inside an intron or not. The trouble is - **to perform validation - you need to...

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

6

I would like to be able to see all the errors, rather than throw an exception on the 1st one Say you asked to validate 'NM_000059.4(BRCA2):c.-40+1G>C' Now, I know -...

Fix for issue #178 While changing superclasses, I also removed Python2 objects, went with Python3 classes

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

4

The current design uses Parsley to define the correct grammar only, which leads to a "syntax error" on some common mistakes. If we modified the grammar parser to include common...

mitochondria (m.) assembly mapping

7

RefSeq does not have MT transcripts, but Ensembl does, eg [ENST00000361381.2](https://grch37.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000198886;r=MT:10760-12137;t=ENST00000361381) There is currently no "m" (ie m_to_c) etc methods in AssemblyMapper, so you can't convert these easily. Q. Should...

Fix for issue #722

Will make a pull request w/tests shortly Some obscure edge cases I've run into: **Case sensitivity** The [VCF format](https://samtools.github.io/hts-specs/VCFv4.1.pdf) for ref/alt says that "Each base must be one of A,C,G,T,N...

Give table example in README.md

1

Thanks for the plugin! I think it would be good to add an example markdown table to the README.md Maybe I'm dumb, but I tried: ``` | foo | bar...