Expected behavior

We should add some functions

BioAlignments.alignment(::Haplotype{S,T}) where {S,T}
BioAlignments.cigar(::Haplotype{S,T}) where {S,T}

which would return the PairwiseAlignment or String representing the alignment.

Current behavior

Doesn't exist

Possible implementation

~

Context

Haplotypes contain, at their heart, an alignment between the variant strand and the reference strand. There is currently no way to get this information out.

Link to your project

No response