The current behavior is entirely correct, but it doesn't let me compare alignments that have matching against those that don't. I propose a new function
remove_match_ops(::T) where {T<:Union{String,Alignment,AlignedSequence,PairwiseAlignment,PairwiseAlignmentResult}}
that would remove the = (sequence match) and X (sequence mismatch) operations from the CIGAR of the alignment and return a T where those operations would be replaced by M (match) operations and adjacent match operations merged.
Expected Behavior
I would like a way to tell if the two alignments are the same regardless of sequence, such that
Current Behavior
:point_up: This behavior is correct!
Possible Solution / Implementation
The current behavior is entirely correct, but it doesn't let me compare alignments that have matching against those that don't. I propose a new function
that would remove the
=
(sequence match) andX
(sequence mismatch) operations from the CIGAR of the alignment and return aT
where those operations would be replaced byM
(match) operations and adjacent match operations merged.