add contig sizes (for reference genome) to VCF header

schneebergerlab / syri

Synteny and Rearrangement Identifier

https://schneebergerlab.github.io/syri/

MIT License

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add contig sizes (for reference genome) to VCF header #237

Closed mparker2 closed 4 months ago

mnshgl0110 commented 4 months ago

@mparker2 I do not think it is a good practice to use an internal object (in this case data) to describe the input files (chromosome lengths). A bug in data could result in embarrassing errors in VCF and I would prefer to avoid that. Therefore, the contig lengths for VCF would need to be calculated from the input ref.fa

mparker2 commented 4 months ago

sure, something like this then? I haven't tested it

mnshgl0110 commented 4 months ago

Looks great. Thanks a lot @mparker2