VCF file input

[c0rbeau]

Hello. When I try to run the software with vcf file input. I get the following error.

julia> using OrdinalGWAS

julia> const datadir = normpath(joinpath(dirname(pathof(OrdinalGWAS)), "../data/"))
"C:\\Users\\Corbeau\\.julia\\packages\\OrdinalGWAS\\g7QpK\\data\\"

julia> ordinalgwas(@formula(y ~ sex), datadir * "vcf_example.csv",
           datadir * "vcf_test"; geneticformat = "VCF", vcftype = :DS)
ERROR: MethodError: no method matching copy_ds!(::Vector{Union{Missing, Float64}}, ::GeneticVariation.VCF.Reader; model=:additive, impute=true, record_chr=Any[#undef], record_pos=Any[#undef], record_ids=Any[#undef])
Closest candidates are:
  copy_ds!(::Union{AbstractArray{Union{Missing, T}, 1}, AbstractArray{Union{Missing, T}, 2}}, ::VariantCallFormat.Reader; key, model, impute, center, scale, msg, sampleID, record_chr, record_pos, record_ids, record_ref, record_alt) where T<:Real at C:\Users\Corbeau\.julia\packages\VCFTools\F07kI\src\convert.jl:651
Stacktrace:
 [1] WARNING: both OrdinalMultinomialModels and Distributions export "cor"; uses of it in module OrdinalGWAS must be qualified
WARNING: both OrdinalMultinomialModels and Distributions export "loglikelihood"; uses of it in module OrdinalGWAS must be qualified
(::OrdinalGWAS.var"#28#34"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLoptSolver, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrames.DataFrame, GeneticVariation.VCF.Reader})(io::IOStream)
   @ OrdinalGWAS C:\Users\Corbeau\.julia\packages\OrdinalGWAS\g7QpK\src\gwas.jl:707
 [2] makestream(::OrdinalGWAS.var"#28#34"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLoptSolver, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrames.DataFrame, GeneticVariation.VCF.Reader}, ::String, ::Vararg{String, N} where N)
   @ SnpArrays C:\Users\Corbeau\.julia\packages\SnpArrays\pDgJb\src\codec.jl:31
 [3] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, vcffile::String, nsamples::Int64, vcftype::Symbol; analysistype::String, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1}, snpinds::Nothing, vcfrowinds::UnitRange{Int64}, solver::NLoptSolver, verbose::Bool, snpset::Nothing, e::Nothing)
   @ OrdinalGWAS C:\Users\Corbeau\.julia\packages\OrdinalGWAS\g7QpK\src\gwas.jl:678
 [4] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, geneticfile::String; analysistype::String, geneticformat::String, vcftype::Symbol, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1}, snpinds::Nothing, geneticrowinds::Nothing, solver::NLoptSolver, verbose::Bool, snpset::Nothing, e::Nothing)
   @ OrdinalGWAS C:\Users\Corbeau\.julia\packages\OrdinalGWAS\g7QpK\src\gwas.jl:218
 [5] ordinalgwas(nullformula::FormulaTerm{Term, Term}, nulldf::DataFrames.DataFrame, geneticfile::String; nullfile::String, link::LogitLink, solver::NLoptSolver, verbose::Bool, kwargs::Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:geneticformat, :vcftype), Tuple{String, Symbol}}})
   @ OrdinalGWAS C:\Users\Corbeau\.julia\packages\OrdinalGWAS\g7QpK\src\gwas.jl:126
 [6] #ordinalgwas#3
   @ C:\Users\Corbeau\.julia\packages\OrdinalGWAS\g7QpK\src\gwas.jl:105 [inlined]
 [7] top-level scope
   @ REPL[4]:1

julia>

[Hua-Zhou]

I can run the above code without error. My environment:

Julia Version 1.6.0
Commit f9720dc2eb (2021-03-24 12:55 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.6.0)
  CPU: Intel(R) Core(TM) i7-6920HQ CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)
Environment:
  JULIA_NUM_THREADS = 4
  JULIA_EDITOR = code

@c0rbeau Maybe you can try to update the VCFTools package? My package versions are

(@v1.6) pkg> st
      Status `~/.julia/environments/v1.6/Project.toml`
  [6db4b851] BGEN v0.1.3 `https://github.com/OpenMendel/BGEN.jl#main`
  [488c2830] BSplines v0.3.2
  [a93c6f00] DataFrames v0.22.7
  [31c24e10] Distributions v0.24.18
  [c47b6ae2] GLMCopula v0.1.0 `~/.julia/dev/GLMCopula`
  [7073ff75] IJulia v1.23.2
  [f87dc7a8] JointModelMoM v0.0.1 `~/.julia/dev/JointModelMoM`
  [00428148] OrdinalGWAS v0.5.3 `https://github.com/OpenMendel/OrdinalGWAS.jl#master`
  [b51826c6] OrdinalMultinomialModels v0.3.4 `https://github.com/OpenMendel/OrdinalMultinomialModels.jl#master`
  [91a5bcdd] Plots v1.12.0
  [6f49c342] RCall v0.13.10
  [4e780e97] SnpArrays v0.3.9 `https://github.com/OpenMendel/SnpArrays.jl#master`
  [a620830f] VCFTools v0.2.2 `https://github.com/OpenMendel/VCFTools.jl#master`

[biona001]

The code works for me as well. GeneticVariation has been depreciated a long time ago, so updating VCFtools.jl by ]up VCFTools should resolve the problem