Peter Krusche

I think it's probably worth trying to retrieve the intermediate file. Hap.py has two command line options for doing that: `--keep-scratch` will not delete intermediate files, `--scratch-prefix ` will write...

Could it be that you're using a reference Fasta that uses numeric chromosome names (no chr) but some inputs (truth files) which do? Hap.py will only add a chr prefix...

I think the problem will be that the variant is filtered in the VCF file. Filtered variants on the truth side of the comparison will be dropped (there is a...

Thanks for reporting this issue! I think this should be specific to the xcmp comparison engine that hap.py uses by default -- using the `--engine=vcfeval` command line option should fix...

This is probably caused by an outdated version of g++ being used (< 4.9.x), see also https://github.com/Illumina/hap.py/issues/13#issuecomment-286348476

(the key thing is the `regex_error` in the output -- this happens with older versions of g++)

Thanks for reporting this + the repro.vcf file. It seems like the hom-ref blocks in the file are causing this (although I don't fully understand how yet). Preprocessing with `bcftools...

Which version of g++ are you using to compile hap.py? Older versions than 4.9.2 can cause issues with their implementation of std::regex.

@nh13 @stephenturner @wdecoster hap.py has issues with gcc < 4.9.x (regex errors) and apparently also with 7.3 (unit test failure). From what I can tell, Bioconda has been in the...

Seems you’re missing libbz2-dev for building boost. You could supply your own Boost build (the readme has instructions) or install libbz2-dev.