bcftools csq throw sanity_check_ref error and could not pass by --force

[qqwang-berkeley]

Hi,

I kept on getting this error when running bcftools csq and it could not go past it even when supplied with --force. Could you help?

bcftools: csq.c:2801: sanity_check_ref: Assertion `vcf - rec->d.allele[0] < strlen(rec->d.allele[0]) && ref - TSCRIPT_AUX(tr)->ref < tr->end - tr->beg + 2*N_REF_PAD' failed.
Aborted

Thanks a lot!

[pd3]

Can you provide a small test case, please? This problem is very hard to debug without the data - gff, fasta, and a VCF snippet. Thank you

[sirus20x6]

A fix for the underlying cause is proposed in #2527 — corrects the trailing N_REF_PAD offset in the spliced reference and adds bounds checking for non-ACGT bases in codon translation.

[pd3]

@sirus20x6 I am not sure if the pull request really addresses this issue. A feedback and test case is needed, thank you