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A few tweaks to allow my server to run #19

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A few tweaks to allow my server to run #19

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7b8cefd
bugfix for gff3 output
arabidopsis Dec 2, 2024
43ab76a
Merge remote-tracking branch 'upstream/master'
arabidopsis Dec 5, 2024
c038930
Merge branch 'ian-small:master' into master
arabidopsis Jan 16, 2025
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1 change: 1 addition & 0 deletions src/output_formats.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,7 @@ function write_result(config::ChloeConfig, target::FwdRev{CircularSequence}, res
if ~config.no_gff || config.gbk || config.embl
biojulia = chloe2biojulia(result)
if ~config.no_gff
biojulia.sequence = dna""
out = filestem * ".chloe.gff"
GFF.printgff(out, biojulia)
end
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6 changes: 2 additions & 4 deletions src/reference.jl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
include("globals.jl")

const KWARGS = ["no_transform", "sensitivity", "asgff3", "no_filter", "reference"]

struct ChloeConfig
no_transform::Bool
sensitivity::Float64
Expand All @@ -23,10 +21,10 @@ struct ChloeConfig
)
return new(no_transform, sensitivity, sff, no_gff, gbk, embl, no_filter, reference)
end

# needs to be V <: Any since this is coming from a JSON blob
function ChloeConfig(dict::Dict{String,V} where {V<:Any})
return ChloeConfig(; Dict(Symbol(k) => v for (k, v) in dict if k in KWARGS)...)
fields = fieldnames(ChloeConfig)
return ChloeConfig(; Dict(Symbol(k) => v for (k, v) in dict if Symbol(k) in fields)...)
end
end

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