rename convert_gt to convert_bgen_gt

Author: biona001

src/wrapper.jl

@@ -327,7 +327,7 @@ function cross_validate(
 end
 
 """
-    convert_gt(t::Type{T}, b::Bgen)
+    convert_bgen_gt(t::Type{T}, b::Bgen)
 
 Imports BGEN genotypes and chr/sampleID/pos/snpID/ref/alt into numeric arrays.
 Genotypes are centered and scaled to mean 0 variance 1. Missing genotypes will
@@ -340,7 +340,7 @@ be replaced with the mean. Assumes every variant is biallelic (ie only 1 alt all
 # Output
 - `G`: matrix of genotypes with type `T`. 
 """
-function convert_gt(t::Type{T}, b::Bgen) where T <: Real
+function convert_bgen_gt(t::Type{T}, b::Bgen) where T <: Real
     n = n_samples(b)
     p = n_variants(b)
 
@@ -428,7 +428,7 @@ will be stored in double precision matrices (64 bit per entry).
 """
 function parse_genotypes(tgtfile::AbstractString, dosage=false)
     if (endswith(tgtfile, ".vcf") || endswith(tgtfile, ".vcf.gz"))
-        f = dosage ? VCFTools.convert_ds : VCFTools.convert_gt
+        f = dosage ? convert_ds : convert_gt
         X, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = 
             f(Float64, tgtfile, trans=false, 
             save_snp_info=true, msg = "Importing from VCF file...")
@@ -443,7 +443,7 @@ function parse_genotypes(tgtfile::AbstractString, dosage=false)
             tgtfile[1:end-5] * ".sample" : nothing
         indexfile = isfile(tgtfile * ".bgi") ? tgtfile * ".bgi" : nothing
         bgen = Bgen(tgtfile; sample_path=samplefile, idx_path=indexfile)
-        X, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = MendelIHT.convert_gt(Float64, bgen)
+        X, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = MendelIHT.convert_bgen_gt(Float64, bgen)
     elseif isplink(tgtfile)
         dosage && error("PLINK files detected but dosage = true!")
         X = SnpArrays.SnpData(tgtfile)

test/wrapper_test.jl

@@ -173,6 +173,7 @@ end
         rm("cviht.summary.txt", force=true)
         rm("iht.summary.txt", force=true)
         rm("iht.beta.txt", force=true)
+        rm("iht.cov.txt", force=true)
     catch
         println("Unsuccessful deletion of intermediate files generated in" * 
             " unit tests! Windows users can remove these files manually " * 
@@ -183,14 +184,14 @@ end
 @testset "read BGEN and VCF" begin
     cd(normpath(MendelIHT.datadir()))
     xtrue = convert(Matrix{Float64}, SnpArray("normal.bed"), center=true, scale=true, impute=true)
-    @time xbgen, _ = MendelIHT.convert_gt(Float64, Bgen("normal.bgen"))
+    @time xbgen, _ = MendelIHT.convert_bgen_gt(Float64, Bgen("normal.bgen"))
     @test all(xbgen .≈ xtrue)
     # BGEN wrapper
     @time xbgen, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = MendelIHT.parse_genotypes("normal.bgen")
     @test all(xbgen .≈ xtrue)
     # VCF wrapper
-    @time xbgen, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = MendelIHT.parse_genotypes("normal.vcf.gz")
-    @test all(xbgen .≈ xtrue)
+    @time xvcf, X_sampleID, X_chr, X_pos, X_ids, X_ref, X_alt = MendelIHT.parse_genotypes("normal.vcf.gz")
+    @test all(xvcf .≈ xtrue)
     # Run IHT on wrapper
     result_plink = iht("normal", 10, Normal, phenotypes="phenotypes.txt", verbose=true)
     result_vcf = iht("normal.vcf.gz", 10, Normal, phenotypes="phenotypes.txt", verbose=true)