AlignCheckCommand::AlignCheckCommand(string option){
try {
abort = false;
+ haderror = 0;
//allow user to run help
if(option == "help") { help(); abort = true; }
if (seq.getName() != "") {
statData data = getStats(seq.getAligned());
+ if (haderror == 1) { break; }
+
out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
}
statData data;
sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
- int seqLength = sequence.length();
- for(int i=1;i<seqLength;i++){
+ int length = sequence.length();
+
+ if (length != seqLength) { mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); mothurOutEndLine(); haderror = 1; return data; }
+
+ for(int i=1;i<length;i++){
if(structMap[i] != 0){
if(sequence[i] == 'A'){
if(sequence[structMap[i]] == 'T') { data.tilde++; }