fixing BCF tests

Author: abhinavsns

src/bcf/bcf.jl

@@ -12,7 +12,13 @@ module BCF
 import GeneticVariation.VCF
 import BGZFStreams
 import TranscodingStreams
-import BioGenerics.IO: AbstractReader, AbstractWriter, stream
+using BioGenerics
+import BioGenerics: BioGenerics, isfilled
+import BioGenerics.Exceptions: MissingFieldException, missingerror
+
+function parsehex(str)
+    return map(x -> parse(UInt8, x, base=16), split(str, ' '))
+end
 
 include("record.jl")
 include("reader.jl")

src/bcf/reader.jl

@@ -5,7 +5,7 @@
 #
 # This file is a part of BioJulia.
 # License is MIT: https://github.com/BioJulia/GeneticVariation.jl/blob/master/LICENSE
-struct Reader{T<:IO} <: AbstractReader
+struct Reader{T<:IO} <: BioGenerics.IO.AbstractReader
     version::Tuple{UInt8,UInt8}  # (major, minor)
     header::VCF.Header
     stream::BGZFStreams.BGZFStream{T}
@@ -38,7 +38,7 @@ function Reader(input::IO)
     data = read(stream, l_header)
 
     # parse VCF header
-    vcfreader = VCF.Reader(BufferedStreams.BufferedInputStream(data))
+    vcfreader = VCF.Reader(IOBuffer(data))
 
     return Reader((major, minor), vcfreader.header, stream)
 end
@@ -55,9 +55,15 @@ end
     header(reader::BCF.Reader)::VCF.Header
 Get the header of `reader`.
 """
-
 function header(reader::Reader)
-    return header(reader)
+    return reader.header
+end
+
+function Base.close(reader::Reader)
+    if reader.stream isa IO
+        close(reader.stream)
+    end
+    return nothing
 end
 
 function Base.read!(reader::Reader, record::Record)

src/bcf/writer.jl

@@ -6,7 +6,7 @@
 # This file is a part of BioJulia.
 # License is MIT: https://github.com/BioJulia/GeneticVariation.jl/blob/master/LICENSE
 
-struct Writer{T<:IO} <: AbstractWriter
+struct Writer{T<:IO} <: BioGenerics.IO.AbstractWriter
     stream::BGZFStreams.BGZFStream{T}
 end
 
@@ -43,3 +43,10 @@ function Base.write(writer::Writer, record::Record)
     n += write(writer.stream, record.data)
     return n
 end
+
+function Base.close(writer::Writer)
+    if writer.stream isa IO
+        close(writer.stream)
+    end
+    return nothing
+end

src/vcf/reader.jl

@@ -111,7 +111,6 @@ function Base.read!(rdr::Reader, record::Record)
 
     rdr.state.state = cs
     rdr.state.linenum = ln
-    @info rdr.state.stream, "Line $(ln)"
     rdr.state.filled = found
 
     if found

test/bcf.jl

@@ -8,7 +8,7 @@
     record.sharedlen = 0x1c
     record.indivlen = 0x00
     # generated from bcftools 1.3.1 (htslib 1.3.1)
-    record.data = parsehex("00 00 00 00 ff ff ff ff 01 00 00 00 01 00 80 7f 00 00 01 00 00 00 00 00 07 17 2e 00")
+    record.data = BCF.parsehex("00 00 00 00 ff ff ff ff 01 00 00 00 01 00 80 7f 00 00 01 00 00 00 00 00 07 17 2e 00")
     record.filled = 1:lastindex(record.data)
     @test BCF.chrom(record) == 1
     record = BCF.Record(record)
@@ -35,7 +35,7 @@
 
     bcfdir = path_of_format("BCF")
     reader = BCF.Reader(open(joinpath(bcfdir, "example.bcf")))
-    let header = header(reader)
+    let header = BCF.header(reader)
         @test length(findall(header, "fileformat")) == 1
         @test findall(header, "fileformat")[1] == VCF.MetaInfo("##fileformat=VCFv4.2")
         @test length(findall(header, "FORMAT")) == 4
@@ -62,12 +62,14 @@
     close(reader)
 
     # round-trip test
-    for specimen in YAML.load_file(joinpath(bcfdir, "index.yml"))
+    bcfdir = path_of_format("BCF")
+    data = TOML.parsefile(joinpath(bcfdir, "index.toml"))
+    for specimen in data["valid"]
         filepath = joinpath(bcfdir, specimen["filename"])
         records = BCF.Record[]
         reader = open(BCF.Reader, filepath)
         output = IOBuffer()
-        writer = BCF.Writer(output, header(reader))
+        writer = BCF.Writer(output, BCF.header(reader))
         for record in reader
             write(writer, record)
             push!(records, record)

test/vcf.jl

@@ -252,8 +252,6 @@
 
     # round-trip test
     vcfdir = path_of_format("VCF")
-    # 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"]
@@ -277,7 +275,3 @@
         @test records == records2
     end
 end
-
-function parsehex(str)
-    return map(x -> parse(UInt8, x, base = 16), split(str, ' '))
-end