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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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diagnostic plot fails when "-ibdonly" flag used #277

Closed shajoezhu closed 6 years ago

shajoezhu commented 6 years ago

Describe the bug dEploid version: b23686108791de3fb6276fbc09ce4d1150f37e17

Error in xy.coords(x, y) : 'x' and 'y' lengths differ Calls: fun.interpretDEploid.1 ... plotWSAFvsPLAF -> points -> points.default -> plot.xy -> xy.coords Execution halted

fails when use interpretDEploid.r script. This is WSAF vs PLAF fails because of the different number of points, in the new implementation site selection was done within DEploid, when plot, should match the points according to the positions, exclude file is probably not very helpful anymore

shajoezhu commented 6 years ago

i consider not to use ibdonly in the future. This bug is no longer valide