fix calls to _ishet

BioJulia · Oct 29, 2021 · b8dfe9e · b8dfe9e
1 parent 09e9b79
commit b8dfe9e
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/src/Heterozygosity.jl b/src/Heterozygosity.jl
@@ -24,13 +24,13 @@ Given a `GenoArray`, count the number of times `allele` appears in the
 homozygous state.
 """
 function counthom(geno::T, allele::U) where T<:GenoArray where U <: Signed
-    mapreduce(i -> ishom(i, allele), +, skipmissing(geno))
+    mapreduce(i -> _ishom(i, allele), +, skipmissing(geno))
 end
 
 function counthom(geno::T, allele::AbstractVector{U}) where T<:GenoArray where U<:Integer
     tmp = skipmissing(geno)
     isempty(tmp) && return fill(0, length(allele))
-    map(_allele -> mapreduce(i -> ishom(i, _allele), +, tmp), allele)
+    map(_allele -> mapreduce(i -> _ishom(i, _allele), +, tmp), allele)
 end
 
 """

diff --git a/src/PopGen.jl b/src/PopGen.jl
@@ -39,17 +39,19 @@ module PopGen
 using Reexport
 using PopGenCore
 @reexport module PopGenCore
-    export PopData, PopDataInfo, GenoArray, Genotype, SNP, Msat, genodata, sampleinfo, locusinfo
+    export PopData, PopDataInfo, GenoArray, Genotype, SNP, Msat
+    export genodata, metadata, info
     export isbiallelic, ishom, ishet
     export delimited, csv, genepop, vcf, bcf, @nancycats, @gulfsharks
-    export sampleinfo, locusinfo, samplenames, loci
+    export sampleinfo, sampleinfo!, locusinfo, locusinfo!, samplenames, loci
     export copy, size, sort, dropmonomorphic, dropmonomorphic!
     export dropmultiallelic, dropmultiallelic!
-    export locations, locations!
+    export locationdata, locationdata!
     export locidataframe, locimatrix
-    export genotypes, genotypes, genotype
+    export genotypes, genotypes
     export populations, populations!
-    export exclude, remove, omit, exclude!, remove!, omit!, keep, keep!, filter, filter!
+    export exclude, remove, omit, exclude!, remove!, omit!, keep, keep!
+    export filter, filter!
 end
 @reexport import PopGenCore: read, write
 

diff --git a/test/heterozygosity.jl b/test/heterozygosity.jl
@@ -21,7 +21,7 @@ testarray = cats.genodata.genotype[1:10]
     end
 
     @testset "het obs/exp" begin
-        @test PopGen._hetero_obs(testarray) == 0.6
+        @test PopGen._hetero_obs(testarray) == 0.75
         @test PopGen._hetero_exp(testarray) == 0.6015625
     end
 
@@ -43,7 +43,7 @@ testarray = cats.genodata.genotype[1:10]
         tmp = heterozygosity(cats, by = "population")
         @test tmp isa DataFrame
         @test size(tmp) == (17,4)
-        @test samplehet(cats, "N215") == 1/3
+        @test samplehet(cats, "N215") == 3/8
         @test_throws ArgumentError samplehet(cats, "M115")
     end
 end