Contig not in reference FASTA or position out of range (generate_str)

[mbhall88]

I have hit this error

vcfdist/src/dist.cpp

Line 131 in 92db7b5

ERROR("Contig '%s' not in reference FASTA or position out of range (generate_str)", ctg.data());

Specifically, I get

[ERROR vcfdist 12:14:06] Contig 'plasmid_2' not in reference FASTA or position out of range (generate_str)

plasmid_2 is definitely in the reference FASTA, so my only assumption is there some out of range/indexing problem.

Here is a tarball with the files used. They were run with v2.5.2 with the command

vcfdist BPH2947__202310.10x.bcftools.filter.vcf.gz truth.vcf.gz mutreference.fna --largest-variant 50 --credit-threshold 1.0 --realign-truth --realign-query -p BPH2947__202310.without_repetitive_regions. -b BPH2947__202310.unique_regions.bed -mx 234.985

test_data.tar.gz

[TimD1]

Thanks for raising an issue and providing test data!

Sorry for the month delay it took me to get around to this. In the meantime, I finished my PhD requirements, got engaged, and started a new job :)

The error was caused by a variant at position 17 on plasmid_2. When clustering variants, vcfdist tried searching for nearby dependent variants and went off the end of the contig. A simple boundary check fixed it. I hadn't run into this yet since I'm working with human genomes (which don't report variants near chromosome ends due to the telomeres).

[mbhall88]

Oh wow triple congratulations! That's wonderful news. And absolutely no need to apologise.

Oh cool, glad it was a good bug to find. And thanks for the quick fix. I will test it out in the next week or two.