}
}
- if(sequence.find_first_of('-') != string::npos){ // if there are any gaps in the sequence, assume that it is
+ if((sequence.find_first_of('-') != string::npos) || (sequence.find_first_of('.') != string::npos)) { // if there are any gaps in the sequence, assume that it is
setAligned(sequence); // an alignment file
}
setUnaligned(sequence); // also set the unaligned sequence file