GVBase 0.1.2

Author: kose-y

Project.toml

@@ -1,7 +1,7 @@
 name = "PGENFiles"
 uuid = "bbb59ef6-f40c-4dde-a38e-7e7eb74f31f9"
 authors = ["Seyoon Ko <kos@ucla.edu> and contributors"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 BitIntegers = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1"
@@ -14,7 +14,7 @@ Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 BitIntegers = "0.2, 0.3"
 CSV = "0.10"
 DataFrames = "1"
-GeneticVariantBase = "0.1"
+GeneticVariantBase = "0.1.2"
 julia = "1.6"
 
 [extras]

src/PGENFiles.jl

@@ -5,7 +5,7 @@ import Mmap: mmap
 import Base: unsafe_load
 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 Pgen, iterator, n_samples, n_variants, get_genotypes, get_genotypes!
 export alt_allele_dosage, alt_allele_dosage!, ref_allele_dosage, ref_allele_dosage!
 BitIntegers.@define_integers 24

src/dosage.jl

@@ -197,3 +197,8 @@ function _get_difflist_dosage!(buf::Vector{T}, p::Pgen, dl::DiffList,
     end
     return offset + 2 * dl.len
 end
+
+function alt_dosages!(arr::AbstractArray{T}, p::Pgen, v::PgenVariant; 
+        genobuf=Vector{UInt8}(undef, p.header.n_samples), genoldbuf=nothing) where T <: Real
+    alt_allele_dosage!(arr, genobuf, p, v; genoldbuf=genoldbuf)
+end

test/runtests.jl

@@ -86,6 +86,8 @@ end
         @test all(isapprox.(d_bgen, d_pgen; atol=5e-5, nans=true))
         PGENFiles.alt_allele_dosage!(d_pgen, g_pgen, p, v_pgen; genoldbuf=g_pgen_ld)  
         @test all(isapprox.(d_bgen, d_pgen; atol=5e-5, nans=true))
+        GeneticVariantBase.alt_dosages!(d_pgen, p, v_pgen; genobuf=g_pgen, genoldbuf=g_pgen_ld)  
+        @test all(isapprox.(d_bgen, d_pgen; atol=5e-5, nans=true))
         v_rt = v_pgen.record_type & 0x07
         if v_rt != 0x02 && v_rt != 0x03 # non-LD-compressed. See Format description.
             g_pgen_ld .= g_pgen