comment

partitioning/SmithWaterman.cpp

@@ -22,7 +22,7 @@
 #include <sys/time.h>
 using namespace std;
 
-int ind; 
+int ind;
 
 double score_match = 10;
 double score_gap = -7;
@@ -183,7 +183,7 @@ void SmithWaterman(const std::string& seqA, const std::string& seqB, double& adj
 	//for(int j=tick-1;j>=0;j--) cout<<consensus_b[j];
 	//cout<<endl;
 
-	adjusted_score = matrix_max/lengthSeqB;
+	adjusted_score = matrix_max/lengthSeqB; // makes the score between 0 and 10
 	align_start = next_i;
 	align_stop = i_max;