Update to BedGraph v2.3

Project.toml

@@ -14,7 +14,7 @@ TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
 
 [compat]
-Bedgraph = "1.2"
+Bedgraph = "2.3"
 DataValues = "0.4"
 FileIO = "1.0.1"
 IterableTables = "0.9, 0.10, 0.11, 1"

src/BedgraphFiles.jl

@@ -71,16 +71,6 @@ function Base.collect(T::Type, x::BedgraphFile)
     return collect(T, getiterator(x))
 end
 
-function Base.convert(::Type{T}, nt::NamedTuple{(:chrom, :first, :last, :value),Tuple{String,Int64,Int64,R}}) where {R <: Real, T<: Bedgraph.Record}
-    @debug "Convert - strict."
-    return T(nt.chrom, nt.first, nt.last, nt.value)
-end
-
-function Base.convert(::Type{T}, nt::NamedTuple{names,Tuple{String,Int64,Int64,R}}) where {R <: Real, names, T<: Bedgraph.Record}
-    @debug "Convert - names."
-    return T(nt[1], nt[2], nt[3], nt[4])
-end
-
 function Vector{T}(x) where {T <: Bedgraph.Record}
     return collect(T, getiterator(x))
 end
@@ -96,7 +86,7 @@ function save(file::BedgraphFileFormat, records::Vector{<:Bedgraph.Record}; bump
 
     sort!(records)
 
-    header = Bedgraph.generateBasicHeader(records, bump_forward = bump_forward) #TODO: consolidate header generation and determine whether there is a need for bump_forward.
+    header = Bedgraph.generate_basic_header(records, bump_forward = bump_forward) #TODO: consolidate header generation and determine whether there is a need for bump_forward.
 
     return save(file, header, records)
 end

test/runtests.jl

@@ -76,10 +76,6 @@ using .Bag
     # Check return of data from save method.
     @test Bag.records == Bag.records |> save(Bag.tmp_output_path)
 
-    # Check convert
-    @test Bag.record == convert(Bedgraph.Record, (chrom = "chr1", first=1, last=1, value=0))
-    @test Bag.record == convert(Bedgraph.Record, (chrom = "chr1", left=1, right=1, value=0))
-
     @testset "Integrations" begin
         include("integrations/test-Tables.jl")
         include("integrations/test-QueryOperators.jl")