Mark const fields as const

BioJulia · Oct 17, 2024 · 8199a40 · 8199a40
1 parent 552aeb0
commit 8199a40
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 12 deletions.
diff --git a/src/fasta/reader.jl b/src/fasta/reader.jl
@@ -39,18 +39,18 @@ AGA
 ```
 """
 mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
-    stream::S
+    const stream::S
+    const record::Record
     automa_state::Int
     # set to typemin(Int) if reader uses seek, then the linenum is
     # irreversibly lost.
     encoded_linenum::Int
     index::Union{Index, Nothing}
-    record::Record
     copy::Bool
 
     function Reader{T}(io::T, index::Union{Index, Nothing}, copy::Bool) where {T <: TranscodingStream}
         record = Record(Vector{UInt8}(undef, 2048), 0, 0, 0)
-        new{T}(io, 1, 1, index, record, copy)
+        new{T}(io, record, 1, 1, index, copy)
     end
 end
 

diff --git a/src/fasta/record.jl b/src/fasta/record.jl
@@ -32,7 +32,7 @@ true
 mutable struct Record
     # Data contains the description, then the sequence immediately after
     # without newlines, or the initial > symbol, and then any unused trailing bytes
-    data::Vector{UInt8}
+    const data::Vector{UInt8}
 
     # These lengths are in bytes, not chars
     # Identifier is data[1:identifier_len]

diff --git a/src/fasta/writer.jl b/src/fasta/writer.jl
@@ -26,9 +26,9 @@ end
 ```
 """
 mutable struct Writer{S <: TranscodingStream} <: BioGenerics.IO.AbstractWriter
-    output::S
+    const output::S
     # maximum sequence width (no limit when width ≤ 0)
-    width::Int
+    const width::Int
 
     function Writer{S}(output::S, width::Int) where {S <: TranscodingStream}
         finalizer(new{S}(output, width)) do writer

diff --git a/src/fastq/reader.jl b/src/fastq/reader.jl
@@ -36,15 +36,15 @@ Int8[73, 74, 26, 60]
 ```
 """
 mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
-    stream::S
+    const stream::S
+    const record::Record
     automa_state::Int
     linenum::Int
-    record::Record
     copy::Bool
 
     function Reader{T}(io::T, copy::Bool) where {T <: TranscodingStream}
         record = Record(Vector{UInt8}(undef, 2048), 0, 0, 0)
-        new{T}(io, 1, 1, record, copy)
+        new{T}(io, record, 1, 1, copy)
     end
 end
 

diff --git a/src/fastq/record.jl b/src/fastq/record.jl
@@ -36,7 +36,7 @@ mutable struct Record
     # all rest, including newlines and the @ and + symbol, are not stored.
     # The second description after + must be identical to first description.
     # The quality is not corrected for offset, i.e. it is stored as it in the input file
-    data::Vector{UInt8}
+    const data::Vector{UInt8}
 
     # In bytes, not chars
     identifier_len::Int32

diff --git a/src/fastq/writer.jl b/src/fastq/writer.jl
@@ -27,8 +27,8 @@ end
 ```
 """
 mutable struct Writer{S <: TranscodingStream} <: BioGenerics.IO.AbstractWriter
-    output::S
-    quality_header::UInt8 # 0x00: No, 0x01: Yes, 0x02: Same as when read
+    const output::S
+    const quality_header::UInt8 # 0x00: No, 0x01: Yes, 0x02: Same as when read
 
     function Writer{S}(output::S, quality_header::UInt8) where {S <: TranscodingStream}
         finalizer(new{S}(output, quality_header)) do writer