Set BioSequences compat

Project.toml

@@ -16,8 +16,10 @@ BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 [extensions]
 StringViewsExt = "StringViews"
 
+# Note: We intentionally have strict compat on BioSequences because Kmers
+# reaches into the internals of BioSequences.
 [compat]
-BioSequences = "3.1.3"
+BioSequences = "~3.4.1"
 Random = "1.10"
 julia = "1.10"
 StringViews = "1"

src/iterators/SpacedKmers.jl

@@ -3,7 +3,11 @@
 
 Iterator of kmers with step size. `J` signifies the step size, `S`
 the type of the underlying sequence, and the eltype of the iterator
-is `Kmer{A, K, N}` with the appropriate `N`
+is `Kmer{A, K, N}` with the appropriate `N`.
+
+For example, a `SpacedKmers{AminoAcidAlphabet, 3, 5, Vector{UInt8}}` sampling
+over `seq::Vector{UInt8}` will sample all kmers corresponding to
+`seq[1:3], seq[6:8], seq[11:13]` etc.
 
 See also: [`each_codon`](@ref), [`FwKmers`](@ref)
 

src/iterators/UnambiguousKmers.jl

@@ -1,12 +1,15 @@
 """
     UnambiguousKmers{A <: TwoBit, K, S}
 
-Iterator of 2-bit nucleic acid kmers. This differs from `FwKmers` in that any kmers
-containing ambiguous nucleotides are skipped, whereas using `FwKmers`, they result
-in an error.
-
-Can be constructed more conventiently with the constructors `UnambiguousDNAMers{K}(s)`
-and `UnambiguousRNAMers{K}(s)`.
+Iterator of `(kmer, index)`, where `kmer` are 2-bit nucleic acid kmers in the
+underlying sequence, and `index::Int` the starting position of the kmer in the
+sequence.
+The extracted kmers differ from those of `FwKmers` in that any kmers
+containing ambiguous nucleotides are skipped, whereas using `FwKmers`, encountering
+unambiguous nucleotides result in an error.
+
+This iterator can be constructed more conventiently with the constructors
+`UnambiguousDNAMers{K}(s)` and `UnambiguousRNAMers{K}(s)`.
 
 !!! note
     To obtain canonical unambiguous kmers, simply call `canonical` on each kmer output