Update for static analysis

Author: jakobnissen

.gitignore

@@ -3,6 +3,7 @@
 *.jl.mem
 .DS_Store
 Manifest.toml
+Manifest-v1.*.toml
 TODO.md
 docs/build
 /.vscode

src/construction_utils.jl

@@ -211,7 +211,7 @@ end
     for i in 0:(S - 1)
         encoding = UInt(BioSequences.extract_encoded_element(seq, from + i))::UInt
         isone(count_ones(encoding)) ||
-            throw_uncertain(Alphabet(kmer), eltype(seq), encoding)
+            throw_uncertain(Alphabet(kmer)::Alphabet, eltype(seq)::Type{<:BioSymbol}, encoding)
         kmer = shift_encoding(kmer, trailing_zeros(encoding) % UInt)
     end
     return kmer

src/tuple_bitflipping.jl

@@ -22,7 +22,7 @@ end
 # the `carry` argument to the right side of the resulting tuple.
 # Returns (new_carry, new_tuple)
 @inline function leftshift_carry(
-        x::Tuple{Vararg{T}},
+        x::Tuple{T, Vararg{T}},
         nbits::Integer,
         carry::T,
     ) where {T <: Unsigned}
@@ -33,7 +33,7 @@ end
 end
 
 @inline function rightshift_carry(
-        x::Tuple{Vararg{T}},
+        x::Tuple{T, Vararg{T}},
         nbits::Integer,
         carry::T,
     ) where {T <: Unsigned}