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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
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Seg fault with vcf #361

Open shajoezhu opened 1 year ago

shajoezhu commented 1 year ago 
dEploid \
        -vcf "${sample}.vcf.gz" \
        -plaf 'Colombia_candidates_PLAF.txt' \
        -panel 'Colombia_candidates_reference_panel.txt' \
        -o "$sample" \
        -best \
        -sigma 2.0
zsh: segmentation fault  dEploid -vcf "${sample}.vcf.gz" -plaf 'Colombia_candidates_PLAF.txt' -panel
shajoezhu commented 1 year ago

Assertion failed: (indexOfChromStarts.size() == this->chrom.size()), function trimming, file src/dEploidIO.cpp, line 992.

shajoezhu commented 1 year ago

this was due to vsqlod set up, default value takes 8. when data is poor, and all been filtered, this needs to be more flexible.