int end = windowSize;
int start = 0;
-
+
if(seqLength < windowSize) { return 0; }
while(start < seqLength){
if(end == -1){ end = seqLength; }
+ //failed first window
+ if (end < windowSize) { return 0; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);