listObservedMutations function does not have "multipleMutation" flag

[Ang Cui]

In createSubstitutionMatrix & createMutabilityMatrix,

  mutations <- listObservedMutations(db, sequenceColumn=sequenceColumn, 
                                     germlineColumn=germlineColumn)

Does not have the multipleMutation flag.

On the other hand, in the following code, the "multipleMutation" flag is not doing anything. It changes codonSeq, but codonSeq is not used afterwards.

 if (!any(codonGL %in% c("N", "-", ".")) & !any(codonSeq %in% c("N", "-", "."))) {
        if (multipleMutation == "independent") { # if independent mutations are included
          codonSeq <- codonGL
          codonSeq[muCodonPos] <- seqAtMutation
        }
        if (!length(grep("N", wrd5))) {
          COUNT[[index]][wrd5]<- COUNT[[index]][wrd5] + 1;
        }
 }

[Ang Cui]

Fixed in c69c730