Merge pull request #117 from zhaotianjing/master

add error message for categorial trait

src/1.JWAS/src/categorical_and_censored_trait/categorical_and_censored_trait.jl

@@ -50,6 +50,14 @@ function categorical_censored_traits_setup!(mme,df)
                     thresholds_all[t] = [tmin; 0; range(1,length=ncategories[t]-1,stop=tmax)]
                 end
             end
+            # check whether the categories are 1,2,3...; otherwise it will cause indexing error
+            category_obs_t     = category_obs[:,t]
+            user_categories    = sort(unique(category_obs_t))
+            correct_categories = collect(1:ncategories[t])
+            if user_categories != correct_categories
+                trait_name = mme.lhsVec[trait_index]
+                error("For categorical trait $trait_name, the categories should be ",correct_categories," ; instead of ",user_categories)
+            end
         end
         # update lower_bound and upper_bound
         update_bounds_from_threshold!(lower_bound,upper_bound,category_obs,thresholds_all,categorical_trait_index)

src/3.GWAS/src/GWAS.jl

@@ -76,11 +76,14 @@ function GWAS(mme,map_file,marker_effects_file::AbstractString...;
     end
 
     window_size_bp = map(Int64,parse(Float64,split(window_size)[1])*1_000_000)
-    mapfile = (header == true ? readdlm(map_file,',',header=true)[1] : readdlm(map_file,','))
+    mapfile = CSV.read(map_file, DataFrame, header = header, types=Dict(1 => String)) #the 1st column (markerID) must be string
     #remove SNPs in mapfile that are not used in Bayesian analysis (e.g., removed in QC)
     snpID    = mme.M[1].markerID
     in_snpID = findall(x -> x ∈ snpID, mapfile[:,1])
     mapfile  = mapfile[in_snpID,:]
+    if length(in_snpID)==0
+        error("Please check the 1st column of the mapfile (i.e., marker ID)")
+    end
 
     chr     = map(string,mapfile[:,2])
     pos     = map(Int64,mapfile[:,3])