A minor point, but maybe this section could be clarified to explain how the M operation is replaced by the =/X convention depending on if WFAlignerGapAffine::getCIGAR() showMismatches is set to true or false. Or perhaps elsewhere. It's a bit confusing that the = is missing from this text: "computes the sequence of alignment operations (i.e., {'M','X','D','I'})"
Hi,
A minor point, but maybe this section could be clarified to explain how the
Moperation is replaced by the=/Xconvention depending on ifWFAlignerGapAffine::getCIGAR()showMismatches is set to true or false. Or perhaps elsewhere. It's a bit confusing that the=is missing from this text: "computes the sequence of alignment operations (i.e., {'M','X','D','I'})"