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Biostar139647 update #229

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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

  • [X ] Code compiles correctly
  • [ ?] All tests passing
  • [ X] Extended the README / documentation, if necessary
  • [ X] Added myself + history to the source file

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