Add a benchmarking file

test/benchmark.jl

@@ -0,0 +1,129 @@
+module TestBenchmarks
+
+using Kmers
+
+extract_kmer(::Type{<:Kmers.AbstractKmerIterator}, x) = x
+extract_kmer(::Type{<:FwRvIterator}, x) = first(x)
+extract_kmer(::Type{<:UnambiguousKmers}, x) = first(x)
+
+function reducer(it)
+    y = 0
+    for i in it
+        y ⊻= extract_kmer(typeof(it), i).data[1]
+    end
+    y
+end
+
+using Random: Xoshiro
+using BioSequences
+rng = Xoshiro(439824)
+
+const N = 10_000_000
+
+const seq_2bit = randseq(DNAAlphabet{2}(), N)
+const seq_4bit = randrnaseq(N)
+const seq_aa = randaaseq(N)
+const data = String(rand(codeunits("AaCcGgTt"), N))
+
+const names = [
+    ("2-bit LongSequence", seq_2bit),
+    ("4-bit LongSequence", seq_4bit),
+    ("AA LongSequence", seq_aa),
+    ("String", data),
+]
+
+println("Time to iterate over $N symbols:\n")
+println("FwKmers")
+for (name, seq) in names[1:3]
+    it = FwKmers{typeof(Alphabet(seq)), 7}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = FwDNAMers{7}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+println("FwRvIterator")
+for (name, seq) in names[1:2]
+    it = FwRvIterator{typeof(Alphabet(seq)), 7}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = FwRvIterator{DNAAlphabet{2}, 7}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+println("CanonicalKmers")
+for (name, seq) in names[1:2]
+    it = CanonicalKmers{typeof(Alphabet(seq)), 7}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = CanonicalDNAMers{7}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+println("UnambiguousKmers")
+for (name, seq) in names[1:2]
+    it = UnambiguousRNAMers{7}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = UnambiguousRNAMers{7}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+println("SpacedKmers, step 5")
+for (name, seq) in names[1:3]
+    it = SpacedKmers{typeof(Alphabet(seq)), 7, 5}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = SpacedDNAMers{7, 5}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+println("SpacedKmers, step 7")
+for (name, seq) in names[1:3]
+    it = SpacedKmers{typeof(Alphabet(seq)), 7, 7}(seq) 
+    y = reducer(it)
+    @time "    " * name reducer(it)
+end
+it = SpacedDNAMers{7, 7}(data)
+y = reducer(it)
+@time "    String" reducer(it)
+
+function unsafe_extract_minimizer(
+    seq::LongDNA{2},
+    i::Int,
+    ::Val{K},
+    ::Val{W},
+) where {K, W}
+    T = derive_type(Kmer{DNAAlphabet{2}, K})
+    kmer = Kmers.unsafe_extract(Kmers.Copyable(), T, seq, i)
+    hash = fx_hash(kmer)
+    for offset in 0:W-2
+        new_kmer = Kmers.unsafe_shift_from(Kmers.Copyable(), kmer, seq, i+K+offset, Val(1))
+        new_hash = fx_hash(new_kmer)
+        if new_hash < hash
+            hash = new_hash
+            kmer = new_kmer
+        end
+    end
+    kmer
+end
+
+function benchmark_minimizer(seq)
+    y = 0
+    for i in 1:20:length(seq)-19
+        mer = unsafe_extract_minimizer(seq, i, Val{8}(), Val{20}())
+        y ⊻= mer.data[1]
+    end
+    y
+end
+
+println("Minimizer")
+benchmark_minimizer(seq_2bit)
+@time "    2-bit LongSequence" benchmark_minimizer(seq_2bit)
+
+end # module