Implement copy! for records

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.1.0]
+### Additions
+* Implement `Base.copy!` for `FASTQRecord` and `FASTARecord`
+
 ## [2.0.1]
 ### Bugfix
 * Fix `Base.read!(::FASTQReader, ::FASTQRecord)` (issue #95)

Project.toml

@@ -1,7 +1,7 @@
 name = "FASTX"
 uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 authors = ["Sabrina J. Ward <[email protected]>", "Jakob N. Nissen <[email protected]>"]
-version = "2.0.1"
+version = "2.1.0"
 
 [weakdeps]
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"

src/fasta/record.jl

@@ -122,6 +122,16 @@ function Base.copy(record::Record)
     )
 end
 
+function Base.copy!(dst::Record, src::Record)
+    n = filled(src)
+    length(dst.data) < n && resize!(dst.data, n)
+    unsafe_copyto!(dst.data, 1, src.data, 1, n)
+    dst.identifier_len = src.identifier_len
+    dst.description_len = src.description_len
+    dst.sequence_len = src.sequence_len
+    dst
+end
+
 function Base.write(io::IO, record::Record)
     data = record.data
     write(io, UInt8('>'))

src/fastq/record.jl

@@ -178,6 +178,16 @@ function Base.copy(record::Record)
     )
 end
 
+function Base.copy!(dst::Record, src::Record)
+    n = filled(src)
+    length(dst.data) < n && resize!(dst.data, n)
+    unsafe_copyto!(dst.data, 1, src.data, 1, n)
+    dst.identifier_len = src.identifier_len
+    dst.description_len = src.description_len
+    dst.has_description_seq_len = src.has_description_seq_len
+    dst
+end
+
 function Base.write(io::IO, record::Record)
     data = record.data
     len = UInt(seqsize(record))

test/fasta/record.jl

@@ -10,11 +10,6 @@
     empty!(record)
     @test record == record2
 
-    # Copying
-    cp = copy(record)
-    @test record == cp
-    @test record.data !== cp.data
-
     # Components of empty records
     @test identifier(record) isa AbstractString
     @test isempty(identifier(record))
@@ -129,6 +124,25 @@ end
     @test sequence(String, cp) == "OOJMQQ"
 end
 
+@testset "Copying" begin 
+    record = parse(Record, ">some_identifier \tmy_description  | text\nAAT\nTA\nCCG")
+    resize!(record.data, 1000)
+    cp = copy(record)
+
+    @test record !== cp
+    @test record == cp
+    @test sequence(record) == sequence(cp)
+    @test identifier(record) == identifier(cp)
+    @test description(record) == description(cp)
+    @test record.data !== cp.data
+
+    record = parse(Record, ">another record\r\nUAGWMPK\nKKLLAAM")
+    @test record != cp
+    copy!(record, cp)
+    @test record !== cp
+    @test record == cp
+end
+
 # Get sequence as String/StringView
 @testset "Get sequence" begin
     record = Record(codeunits("ab cAACCAAGGTTKKKMMMM"), 2, 4, 10)

test/fastq/record.jl

@@ -10,13 +10,6 @@
     empty!(record)
     @test record == record2
 
-    # Copying
-    resize!(record.data, 1000)
-    cp = copy(record)
-    empty!(record.data)
-    @test record == cp
-    @test record.data !== cp.data
-
     # Components of empty records
     @test identifier(record) == ""
     @test description(record) == ""
@@ -122,6 +115,28 @@ end
     end
 end
 
+@testset "Copying" begin 
+    record = parse(Record, "@A\nTGGAA\n+\nJJJAA")
+    resize!(record.data, 1000)
+    cp = copy(record)
+
+    @test record !== cp
+    @test record == cp
+    @test sequence(record) == sequence(cp)
+    @test identifier(record) == identifier(cp)
+    @test description(record) == description(cp)
+    @test quality(record) == quality(cp)
+    @test record.data !== cp.data
+    # Test that we don't unnecessarily copy noncoding data
+    @test length(record.data) > length(cp.data)
+
+    record = parse(Record, "@some other record\r\nTAGA\r\n+\r\nJJJK")
+    @test record != cp
+    copy!(record, cp)
+    @test record !== cp
+    @test record == cp
+end
+
 @testset "Get sequence as String/StringView" begin
     records = map(i -> parse(Record, i), TEST_RECORD_STRINGS)