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make write_vcf handle missing #35

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make write_vcf handle missing #35

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12 changes: 8 additions & 4 deletions src/write.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -68,9 +68,10 @@ end

"""
Helper function for saving the `i`th record (SNP), tracking phase information.
Here `X = X1 + X2`.
Here `X = X1 + X2`. For phased data, X1 and X2 must have entries in {0, 1} (in
particular, there should be no missing data).
"""
function write_snp!(pb::IOBuffer, X1::AbstractMatrix, X2::AbstractMatrix, i::Int)
function write_snp!(pb::IOBuffer, X1::AbstractMatrix{T}, X2::AbstractMatrix{T}, i::Int) where T
x1 = @view(X1[:, i])
x2 = @view(X2[:, i])
n = length(x1)
Expand Down Expand Up @@ -122,7 +123,7 @@ function write_vcf(
ref::AbstractVector{String} = ["A" for i in 1:size(x, 2)],
alt::AbstractVector{String} = ["T" for i in 1:size(x, 2)],
sampleID::AbstractVector{String} = [string(i) for i in 1:size(x, 1)],
SNPids::AbstractVector{String} = ["snp$i" for i in 1:size(x, 2)],
SNPids::AbstractVector{String} = ["." for i in 1:size(x, 2)],
)
n, p = size(x)
io = openvcf(outfile, "w")
Expand Down Expand Up @@ -163,12 +164,15 @@ Here genotypes will be written as
0 => 0/0
1 => 1/0
2 => 1/1
missing => ./.
"""
function write_snp!(pb::IOBuffer, X::AbstractMatrix, i::Int)
x = @view(X[:, i])
n = length(x)
@inbounds for j in 1:n
if x[j] == 0
if ismissing(x[j])
print(pb, "\t./.")
elseif x[j] == 0
print(pb, "\t0/0")
elseif x[j] == 1
print(pb, "\t1/0")
Expand Down