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Use of int8 for variant_contig results in integer overflow with fragmented reference genomes

See original GitHub issue

Many (non human) reference genomes contain 1000s of contigs that have not been assembled into full chromosomes. Currently the variant_contig array is hard coded as int8 (line) which results in integer overflow making it impossible to join variants to their contig.

Issue Analytics

State:
Created 2 years ago
Reactions:1
Comments:10 (1 by maintainers)

Top GitHub Comments

3reactions

jeromekellehercommented, Jun 1, 2021

We should make it an option to specify the dtype for variant_contig probably - even int16 will overflow sometimes. There are lots of VCFs out there with huge numbers of contigs.

Although, I guess this is the sort of thing we should be able to query the IO library for (“how many contigs are there” should be efficiently computable on any indexed VCF), so we should be able to automatically detect the minimal dtype. Even then though, I suppose people might want to manually specify the dtype, for their own reasons.

2reactions

tomwhitecommented, Sep 14, 2021

Nice!

I’ve created a fix in #667. Hopefully we can get that merged soon for you to use.