more rigorous tests for multiple calls for dosage

OpenMendel · May 3, 2023 · 758d453 · 758d453
1 parent 787e0a1
commit 758d453
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diff --git a/src/genotypes.jl b/src/genotypes.jl
@@ -411,6 +411,7 @@ function second_dosage!(data::Vector{<:AbstractFloat}, p::Preamble)
  @inbounds for n in (p.n_samples - p.n_samples % 8 + 1):p.n_samples
  data[n] = 2.0 - data[n]
  end
+
 end
 
 """
@@ -561,6 +562,7 @@ function first_allele_dosage!(b::Bgen, v::Variant;
  if genotypes.minor_allele_dosage && genotypes.minor_idx != 1
  second_dosage!(genotypes.dose, p)
  end
+ genotypes.minor_allele_dosage = (genotypes.minor_idx == 1)
  return v.genotypes.dose
  end
  if (decompressed !== nothing && !is_decompressed) ||
@@ -610,6 +612,7 @@ function first_allele_dosage!(b::Bgen, v::Variant;
  if clear_decompressed
  clear_decompressed!(genotypes)
  end
+ genotypes.minor_allele_dosage = (genotypes.minor_idx == 1)
  return data
 end
 

diff --git a/test/test_minor_allele_dosage.jl b/test/test_minor_allele_dosage.jl
@@ -63,11 +63,22 @@ b = Bgen(
 v = variant_by_rsid(b, "RSID_110")
 @test isapprox(mean(minor_allele_dosage!(b, v)), 0.9621725f0)
 @test isapprox(mean(minor_allele_dosage!(b, v)), 0.9621725f0)
+@test isapprox(mean(first_allele_dosage!(b, v)), 2 - 0.9621725f0)
+@test isapprox(mean(minor_allele_dosage!(b, v)), 0.9621725f0)
+clear!(v)
+@test isapprox(mean(first_allele_dosage!(b, v)), 2 - 0.9621725f0)
+@test isapprox(mean(minor_allele_dosage!(b, v)), 0.9621725f0)
+
 
 # first allele minor
 v = variant_by_rsid(b, "RSID_198")
 @test isapprox(mean(minor_allele_dosage!(b, v)), 0.48411763f0)
 @test isapprox(mean(minor_allele_dosage!(b, v)), 0.48411763f0)
+@test isapprox(mean(first_allele_dosage!(b, v)), 0.48411763f0)
+@test isapprox(mean(minor_allele_dosage!(b, v)), 0.48411763f0)
+clear!(v)
+@test isapprox(mean(first_allele_dosage!(b, v)), 0.48411763f0)
+@test isapprox(mean(minor_allele_dosage!(b, v)), 0.48411763f0)
 end
 
 @testset "mean_impute" begin