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New option to output the CIGAR line of the alignment

Marek Szuba requested to merge github/fork/muffato/cigar_line into master

Created by: muffato

cf RT #475008

  • New option in the gene-tree end-points to output the cigar-lines. Default is False to preserve the current behaviour
  • New option in the homology end-points to output the cigar-lines. Default is True to preserve the current behaviour. I would personally prefer the default to be False but it would mean changing the major version number :/

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