Bump to BioGenerics 0.2 and use new BioGenerics macros

The new BioGenerics `@rdr_str` and `@wtr_str` macros, as well as the `defer`
keyword has been a longstanding FASTX todo.
This change adds this new functionality.

Author: jakobnissen

Project.toml

@@ -3,9 +3,6 @@ uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 authors = ["Sabrina J. Ward <sabrinajward@protonmail.com>", "Jakob N. Nissen <jakobnybonissen@gmail.com>"]
 version = "2.1.3"
 
-[weakdeps]
-BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
@@ -14,22 +11,26 @@ PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 StringViews = "354b36f9-a18e-4713-926e-db85100087ba"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
+[weakdeps]
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+
 [extensions]
 BioSequencesExt = "BioSequences"
 
 [compat]
 Automa = "1"
-BioGenerics = "0.1.2"
+BioGenerics = "0.1.3"
 BioSequences = "3"
 PrecompileTools = "1"
 StringViews = "1"
 TranscodingStreams = "0.9.5"
 julia = "1.6"
 
 [extras]
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReTest = "e0db7c4e-2690-44b9-bad6-7687da720f89"
-BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 
 [targets]
-test = ["BioSequences", "Random", "ReTest"]
+test = ["BioSequences", "Random", "ReTest", "CodecZlib"]

src/FASTX.jl

@@ -2,6 +2,7 @@ module FASTX
 
 using StringViews: StringView
 using Automa: Automa
+using BioGenerics: BioGenerics, defer, @rdr_str, @wtr_str
 
 """
     identifier(record::Record)::AbstractString
@@ -220,6 +221,11 @@ const FASTQReader = FASTQ.Reader
 const FASTAWriter = FASTA.Writer
 const FASTQWriter = FASTQ.Writer
 
+const FASTA_EXTENSIONS = Union{Val{:fa}, Val{:fasta}, Val{:faa}, Val{:fna}}
+
+BioGenerics.readertype(::FASTA_EXTENSIONS, arg) = FASTAReader
+BioGenerics.writertype(::FASTA_EXTENSIONS, arg) = FASTAWriter
+
 if !isdefined(Base, :get_extension)
     include("../ext/BioSequencesExt.jl")
   end
@@ -249,6 +255,11 @@ export
     faidx,
     index!,
     extract,
-    seekrecord
+    seekrecord,
+
+    # Re-export from BioGenerics
+    defer,
+    @rdr_str,
+    @wtr_str
 
 end # module

test/maintests.jl

@@ -1,3 +1,5 @@
+using CodecZlib
+
 # Common tests
 @testset "FASTX" begin
     @testset "Copying to LongSequence" begin
@@ -133,4 +135,4 @@
         @test sequence(fq) == "TAGJKKm"
         @test quality(fq) == "jjkkmmo"
     end
-end
+end