else{ minCompare.weight = 1; }
printErrorData(minCompare, numParentSeqs);
-
+
if(!ignoreSeq){
-
- for(int i=0;i<minCompare.total;i++){
+
+ for(int i=0;i<minCompare.sequence.length();i++){
char letter = minCompare.sequence[i];
errorForward[letter][i] += minCompare.weight;
int numAmbigs = currentSeq.getAmbigBases();
if(numAmbigs > 0){ numAmbigSeqs++; }
- int startPos = currentSeq.getStartPos();
- if(startPos > maxStartPos) { maxStartPos = startPos; }
-
- int endPos = currentSeq.getEndPos();
- if(endPos < minEndPos) { minEndPos = endPos; }
+// int startPos = currentSeq.getStartPos();
+// if(startPos > maxStartPos) { maxStartPos = startPos; }
+//
+// int endPos = currentSeq.getEndPos();
+// if(endPos < minEndPos) { minEndPos = endPos; }
referenceSeqs.push_back(currentSeq);
+
m->gobble(referenceFile);
}
referenceFile.close();