fixing vcf tests

Author: abhinavsns

Project.toml

@@ -27,7 +27,7 @@ julia = "1"
 [extras]
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
 [targets]
-test = ["Test", "FormatSpecimens", "YAML"]
+test = ["Test", "FormatSpecimens", "TOML"]

src/vcf/record.jl

@@ -333,7 +333,7 @@ function Base.copy(rec::Record)
     )
 end
 
-function Base.write(io::IO, rec::Record)
+function Base.write(io::IO, record::Record)
     return unsafe_write(io, pointer(record.data, first(record.filled)), length(record.filled))
 end
 function Base.print(io::IO, record::Record)

src/vcf/writer.jl

@@ -12,8 +12,8 @@
 
 A VCF writer that sends data to a wrapped IO stream.
 """
-mutable struct Writer{T<:IO} <: BioGenerics.IO.AbstractWriter
-    stream::T
+mutable struct Writer <: BioGenerics.IO.AbstractWriter
+    stream::IO
 end
 
 # Convenience constructor: if given a plain IO, wrap it in a NoopStream.
@@ -35,7 +35,7 @@ function Writer(output::IO, header::Header)
 end
 
 # Expose the underlying stream.
-function stream(writer::Writer)
+function BioGenerics.IO.stream(writer::Writer)
     return writer.stream
 end
 

test/runtests.jl

@@ -5,7 +5,7 @@ using Test
 using BioSequences, GeneticVariation
 using TranscodingStreams
 import IntervalTrees: IntervalValue
-import YAML
+import TOML
 using FormatSpecimens
 
 import GeneticVariation.VCF: isfilled, metainfotag, metainfoval, VCF, VCF.Reader, VCF.Writer, VCF.Record

test/vcf.jl

@@ -129,6 +129,7 @@
         @test metainfoval(header.metainfo[1]) == "VCFv4.3"
         @test isempty(header.sampleID)
     end
+    
 
     # realistic header
     data = Vector{UInt8}("""
@@ -222,8 +223,7 @@
     @test VCF.genotype(record, 2, "GT") == "0/1"
     @test VCF.genotype(record, 1:2, "GT") == ["0|0", "0/1"]
     @test VCF.genotype(record, :, "GT") == VCF.genotype(record, 1:2, "GT")
-    @test occursin(r"^GeneticVariation.VCF.Record:\n.*", repr(record))
-
+    @test occursin(r"^VCF Record\n.*", repr(record))
     @test read!(reader, record) === record
     @test VCF.chrom(record) == "chr2"
     @test VCF.pos(record) == 4
@@ -252,7 +252,11 @@
 
     # round-trip test
     vcfdir = path_of_format("VCF")
-    for specimen in YAML.load_file(joinpath(vcfdir, "index.yml"))
+    # Parse the TOML file; the file should define an array of tables under the key "specimen"
+    # Parse the TOML file. The file now consists of an array of tables under the key "valid".
+    data = TOML.parsefile(joinpath(vcfdir, "index.toml"))
+
+    for specimen in data["valid"]
         filepath = joinpath(vcfdir, specimen["filename"])
         records = VCF.Record[]
         reader = open(VCF.Reader, filepath)
@@ -269,6 +273,7 @@
         for record in VCF.Reader(IOBuffer(take!(output)))
             push!(records2, record)
         end
+
         @test records == records2
     end
 end