Don't fail on dot (`.`) as entry in AD field.

DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

http://deploid.readthedocs.io/en/latest/index.html

GNU General Public License v3.0

20 stars 10 forks source link

Don't fail on dot (`.`) as entry in AD field. #344

Closed bredelings closed 3 years ago

bredelings commented 3 years ago

Describe the bug

octopus generates VCF files with a . instead of a 0 for AD entries that have no haplotype covering them.

When using octopus VCFs, dEploid gives the error message stoi and quits. Ideally, DEploid would

accept . and set the value to 0.
indicate that the error occurred when parsing a specific field in the VCF.