The "error" flag is not being used when collapsing clonal sequences

Need to add code to properly catch errors.
===================================== In function "calcClonalConsensus"
matClone <- sapply(1:len_shortest, function(i){

    # Identify the nucleotides (in seqs and germline) at the current position
    posNucs = unique(charInputSeqs[i,])
    posGL = charGLSeq[i]
    error = FALSE

    # If the current position is a gap in both germline and the sequence,
    # return a gap
    if(posGL=="-" & sum(!(posNucs%in%c("-","N")))==0 ){
        return(c("-",error))
    }

    # If all the sequences in the clone have the same nucleotide at the current
    # position, return the value at the current positions
    if(length(posNucs)==1)
        return(c(posNucs[1],error))
    else{         
        # if the nucleotides at the current position are not all the same

        # TODO: The error message is not doing anything currently... 
        if("N"%in%posNucs){
            error=TRUE
        }

        # If the current nucleotide matches germline, return germline 
        if(sum(!posNucs[posNucs!="N"]%in%posGL)==0){
            return( c(posGL,error) )
        }else{
            #return( c(sample(posNucs[posNucs!="N"],1),error) )

            # If we look at all nodes (including terminal nodes), sample a nucleotide from the possible
            # nucleotides in the clonal sequences at this position
            if(nonTerminalOnly==0){
                return( c(sample(charInputSeqs[i,charInputSeqs[i,]!="N" & charInputSeqs[i,]!=posGL],1),error) )
            }else{

                # If we look at only non-terminal nodes, we only sample the nucleotides that appear more 
                # than once (this is a quick approximation)
                posNucs = charInputSeqs[i,charInputSeqs[i,]!="N" & charInputSeqs[i,]!=posGL]
                posNucsTable = table(posNucs)
                if(sum(posNucsTable>1)==0){
                    return( c(posGL,error) )
                }else{
                    return( c(sample( posNucs[posNucs%in%names(posNucsTable)[posNucsTable>1]],1),error) )
                }
            }

        }
    }
})
return( c2s(matClone[1,]) )
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