feat: Add alignment(::Haplotype) function

src/Haplotype.jl

@@ -250,6 +250,17 @@ function BioAlignments.cigar(hap::Haplotype{S,T}) where {S,T}
     return join(cigar_string, "")
 end
 
+"""
+    alignment(hap::Haplotype)
+
+Gets a `PairwiseAlignment` of the mutated sequence of `hap` mapped to its refernce sequence
+"""
+function BioAlignments.alignment(hap::Haplotype)
+    return PairwiseAlignment(
+        AlignedSequence(reconstruct(hap), Alignment(cigar(hap))), reference(hap)
+    )
+end
+
 """
     translate(hap::Haplotype{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
 

src/SequenceVariation.jl

@@ -20,7 +20,15 @@ TODO now:
 * Add tests
 """
 
-using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP, cigar, sequence
+using BioAlignments:
+    BioAlignments,
+    Alignment,
+    AlignedSequence,
+    PairwiseAlignment,
+    OP_SOFT_CLIP,
+    alignment,
+    cigar,
+    sequence
 using BioGenerics: BioGenerics, leftposition, rightposition
 using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isgap
 using BioSymbols: BioSymbol