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vg construct crashes on chromosome X #1488
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This is my fault, though I'm not sure why this code is getting hit. I added some logic to construct to deal with SVs, but it shouldn't do anything unless you pass I'll work on seeing why this is happening and push a fix. |
OK thanks. The good news is that it is very fast to reproduce. You can even just do something like bcftools view |
It looks like vcflib may not be being built with debug info (-g), which means the line number isn't being reported in the stacktrace. It also looks like construct is unconditionally calling I think the real problem is here: https://github.com/vgteam/vcflib/blob/master/src/Variant.cpp#L210 We're calling We need to fix that line, and preferably harden the whole function (with |
Stack and command line below. The VCF in question is here:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz
Pretty sure this was working up until quite recently...
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