GVBase 0.1.2

Author: kose-y

Project.toml

@@ -1,7 +1,7 @@
 name = "BGEN"
 uuid = "6db4b851-9beb-4b83-9d64-eb1cfb37721d"
 authors = ["Seyoon Ko <kos@ucla.edu> and contributors"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
@@ -18,7 +18,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 CodecZlib = "0.6, 0.7"
 CodecZstd = "0.6, 0.7, 0.8"
-GeneticVariantBase = "0.1"
+GeneticVariantBase = "0.1.2"
 SIMD = "3"
 SQLite = "1"
 SpecialFunctions = "1, 2"

src/BGEN.jl

@@ -7,7 +7,7 @@ import SpecialFunctions: gamma_inc
 import TranscodingStreams: initialize, finalize, buffermem, process, Buffer, Error
 import GeneticVariantBase: GeneticData, Variant, VariantIterator, iterator
 import GeneticVariantBase: chrom, pos, rsid, alleles, alt_allele, ref_allele
-import GeneticVariantBase: maf, hwepval, infoscore, load_values!
+import GeneticVariantBase: maf, hwepval, infoscore, alt_dosages!
 export Bgen, Samples, Variant, Genotypes, Index
 export io, fsize, samples, n_samples, n_variants, compression
 export varid, rsid, chrom, pos, n_alleles, alleles, minor_allele, major_allele
@@ -17,7 +17,7 @@ export first_allele_dosage!, clear!, hardcall, hardcall!
 export select_region, variant_by_rsid, variant_by_pos, variant_by_index
 export rsids, chroms, positions
 export hwe, maf, info_score, counts!
-export VariantIteratorFromStart, VariantIteratorFromOffsets
+export BgenVariantIteratorFromStart, BgenVariantIteratorFromOffsets
 using CodecZlib, CodecZstd, SQLite, SIMD
 include("structs.jl")
 include("iterator.jl")

src/genotypes.jl

@@ -640,6 +640,12 @@ function alt_allele_dosage!(b::Bgen, v::BgenVariant;
     data
 end
 
+function alt_dosages!(arr::AbstractArray{T}, b::Bgen, v::BgenVariant;
+    mean_impute=false, clear_decompressed=false,
+    decompressed=nothing, is_decompressed=false) where T <: Real
+    alt_allele_dosage!(b, v; T=T, mean_impute=mean_impute, clear_decompressed=clear_decompressed, data=arr, decompressed=decompressed, is_decompressed=is_decompressed)
+end
+
 """
     minor_allele_dosage!(b::Bgen, v::BgenVariant; T=Float32,
     mean_impute=false, clear_decompressed=false)

test/test_minor_allele_dosage.jl

@@ -84,6 +84,8 @@ clear!(v)
 clear!(v)
 @test isapprox(mean(BGEN.ref_allele_dosage!(b, v)), 0.48411763f0)
 @test isapprox(mean(BGEN.alt_allele_dosage!(b, v)), 2 - 0.48411763f0)
+clear!(v)
+@test isapprox(mean(GeneticVariantBase.alt_dosages!(Vector{Float32}(undef, n_samples(b)), b, v)), 2 - 0.48411763f0)
 end
 
 @testset "mean_impute" begin