Jean Mainguy comments

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                                            Jean Mainguy

Manage annotation with joined coordinates

## Examples of joined annotations Joined coordinates in annotations can originate from two main sources: frameshift mutations and contig edge overlaps. ### The gene is annotated with a frameshift. ####...

Exception: Reading the gbff file. Expected type is string, given type was '<class 'NoneType'>'

Hi, Thanks for reporting this bug and the workaround. It does not seem complicated to fix. After some testing, the bug also occurs in the `annotate` command (and by extension...

Exception: Reading the gbff file. Expected type is string, given type was '<class 'NoneType'>'

The fix for this issue has been released in v2.1.0.

MAFFT error when running ppanggolin MSA

The PR #229 has been released in v2.1.0

different results ppanggolin projection with gbff or fasta files

Hello, This is surprising in deed. I've been able to replicate the issue. It seems there's a problem with gene ID matching between ppanggolin's internal IDs and the original IDs...

different results ppanggolin projection with gbff or fasta files

The fix for this issue has been released in v2.1.0.

RGP borders not in regions_of_plasticity.tsv

The fix for this issue has been released in v2.1.0.

Clarification about the contents of `gene_to_gene_family.tsv ` from projection

The fix for this issue has been released in v2.1.0.