From 81638d6acefbec49c81a27503722011412ee60db Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Sat, 19 Feb 2022 17:46:16 +0100
Subject: [PATCH] Bump BioSequences/BioSymbols to v3/v5 (#66)

* Bump BioSequences/BioSymbols to v3/v5

* Bump Julia version
---
 Project.toml        | 6 +++---
 src/fasta/record.jl | 8 ++++----
 src/fastq/record.jl | 6 +++---
 test/runtests.jl    | 6 +++---
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/Project.toml b/Project.toml
index c7a9220..9a3cf0a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,7 +4,7 @@ authors = [
     "Sabrina J. Ward <sabrinajward@protonmail.com>",
     "Jakob N. Nissen <jakobnybonissen@gmail.com>"
 ]
-version = "1.2.0"
+version = "1.3.0"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@@ -16,8 +16,8 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 Automa = "0.7, 0.8"
 BioGenerics = "0.1"
-BioSequences = "2.0.2"
-BioSymbols = "4"
+BioSequences = "3"
+BioSymbols = "5"
 TranscodingStreams = "0.9.5"
 julia = "1.6" # LTS
 
diff --git a/src/fasta/record.jl b/src/fasta/record.jl
index 19f149e..3c47ab4 100644
--- a/src/fasta/record.jl
+++ b/src/fasta/record.jl
@@ -243,7 +243,7 @@ If `part` argument is given, it returns the specified part of the sequence.
 function sequence(::Type{S}, record::Record, part::UnitRange{Int}=1:lastindex(record.sequence))::S where S <: BioSequences.LongSequence
     checkfilled(record)
     seqpart = record.sequence[part]
-    return S(record.data, first(seqpart), last(seqpart))
+    return S(@view(record.data[seqpart]))
 end
 
 function sequence(::Type{String}, record::Record, part::UnitRange{Int}=1:lastindex(record.sequence))::String
@@ -343,12 +343,12 @@ function predict_seqtype(seq::Vector{UInt8}, range)
     # the threshold (= 0.95) is somewhat arbitrary
     if (a + c + g + t + u + n) / alpha > 0.95
         if t ≥ u
-            return BioSequences.LongDNASeq
+            return BioSequences.LongDNA{4}
         else
-            return BioSequences.LongRNASeq
+            return BioSequences.LongRNA{4}
         end
     else
-        return BioSequences.LongAminoAcidSeq
+        return BioSequences.LongAA
     end
 end
 
diff --git a/src/fastq/record.jl b/src/fastq/record.jl
index 435501a..1e60fe6 100644
--- a/src/fastq/record.jl
+++ b/src/fastq/record.jl
@@ -271,7 +271,7 @@ If `part` argument is given, it returns the specified part of the sequence.
 function sequence(::Type{S}, record::Record, part::UnitRange{Int}=1:lastindex(record.sequence))::S where S <: BioSequences.LongSequence
     checkfilled(record)
     seqpart = record.sequence[part]
-    return S(record.data, first(seqpart), last(seqpart))
+    return S(@view(record.data[seqpart]))
 end
 
 """
@@ -295,8 +295,8 @@ Get the sequence of `record` as a DNA sequence.
     If you have a sequence already and want to fill it with the sequence
     data contained in a fastq record, you can use `Base.copyto!`.
 """
-function sequence(record::Record, part::UnitRange{Int}=1:lastindex(record.sequence))::BioSequences.LongDNASeq
-    return sequence(BioSequences.LongDNASeq, record, part)
+function sequence(record::Record, part::UnitRange{Int}=1:lastindex(record.sequence))::BioSequences.LongDNA{4}
+    return sequence(BioSequences.LongDNA{4}, record, part)
 end
 
 """
diff --git a/test/runtests.jl b/test/runtests.jl
index 012e030..baae492 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -8,8 +8,8 @@ import BioSequences:
     @dna_str,
     @rna_str,
     @aa_str,
-    LongDNASeq,
-    LongAminoAcidSeq,
+    LongDNA,
+    LongAA,
     LongSequence,
     AminoAcidAlphabet,
     DNAAlphabet,
@@ -37,7 +37,7 @@ import BioSequences:
         @test FASTA.hassequence(record)
         @test FASTA.sequence(LongDNASeq, record) == dna"ACGT"
         @test collect(FASTA.sequence_iter(DNA, record)) == [DNA_A, DNA_C, DNA_G, DNA_T] 
-        @test FASTA.sequence(LongDNASeq, record, 2:3) == LongDNASeq(collect(FASTA.sequence_iter(DNA, record, 2:3))) == dna"CG"
+        @test FASTA.sequence(record, 2:3) == LongDNA{4}(collect(FASTA.sequence_iter(DNA, record, 2:3))) == dna"CG"
         @test FASTA.sequence(String, record) == "ACGT"
         @test FASTA.sequence(String, record, 2:3) == "CG"