When a reference is selected in the clustal alignment, the user can now choose to either keep simple CIGAR matches (cigar M) or decompose them into identical residue match (cigar =) or mismatches (cigar X).
Checklist
[X ] Code compiles correctly
[ ?] All tests passing
[ X] Extended the README / documentation, if necessary
Description
When a reference is selected in the clustal alignment, the user can now choose to either keep simple CIGAR matches (cigar M) or decompose them into identical residue match (cigar =) or mismatches (cigar X).
Checklist