Use one implementation of memcmp

BioJulia · Aug 10, 2022 · e29fdc7 · e29fdc7
1 parent 020e384
commit e29fdc7
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Showing 5 changed files with 6 additions and 11 deletions.
diff --git a/src/FASTX.jl b/src/FASTX.jl
@@ -104,6 +104,10 @@ function truncate(s::AbstractString, len::Integer)
     end
 end
 
+function memcmp(p1::Ptr, p2::Ptr, n::Integer)
+    return ccall(:memcmp, Cint, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), p1, p2, n)
+end
+
 include("fasta/fasta.jl")
 include("fastq/fastq.jl")
 

diff --git a/src/fasta/fasta.jl b/src/fasta/fasta.jl
@@ -20,7 +20,7 @@ import TranscodingStreams: TranscodingStreams, TranscodingStream, NoopStream
 # Trivial use, I only use it here because it's a dep of Automa anyway.
 # Can be removed with no big problems
 using ScanByte: memchr, ByteSet
-import ..FASTX: identifier, description, sequence, UTF8, seqlen, throw_parser_error, truncate
+import ..FASTX: identifier, description, sequence, UTF8, seqlen, throw_parser_error, truncate, memcmp
 
 include("record.jl")
 include("readrecord.jl")

diff --git a/src/fasta/record.jl b/src/fasta/record.jl
@@ -148,10 +148,6 @@ function Base.show(io::IO, record::Record)
     print(io,   "   sequence: \"", truncate(sequence(record), 40), '"')
 end
 
-function memcmp(p1::Ptr, p2::Ptr, n::Integer)
-    return ccall(:memcmp, Cint, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), p1, p2, n)
-end
-
 # TODO: Base's hash does not hash all elements. Do we have a better implementation?
 function Base.hash(record::Record, h::UInt)
     # The description length is informative of the record's content

diff --git a/src/fastq/fastq.jl b/src/fastq/fastq.jl
@@ -13,7 +13,7 @@ import BioGenerics: BioGenerics
 import BioGenerics.Automa: State
 import StringViews: StringView
 import TranscodingStreams: TranscodingStreams, TranscodingStream, NoopStream
-import ..FASTX: identifier, description, sequence, UTF8, seqlen, throw_parser_error, truncate
+import ..FASTX: identifier, description, sequence, UTF8, seqlen, throw_parser_error, truncate, memcmp
 
 include("quality.jl")
 include("record.jl")

diff --git a/src/fastq/record.jl b/src/fastq/record.jl
@@ -212,11 +212,6 @@ function Base.show(io::IO, record::Record)
     print(io,   "      quality: \"", truncate(quality(record), 40), '"')
 end
 
-function memcmp(p1::Ptr, p2::Ptr, n::Integer)
-    return ccall(:memcmp, Cint, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), p1, p2, n)
-end
-
-
 # Accessor functions
 # ------------------