#include <map>
#include <string>
#include <list>
+#include <string.h>
//math
#include <cmath>
#include <sys/wait.h>
#include <sys/time.h>
#include <sys/resource.h>
+ #include <sys/stat.h>
#include <unistd.h>
#ifdef USE_READLINE
seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
~seqDist() {}
};
+/************************************************************/
+struct distlinePair {
+ int start;
+ int end;
+
+};
+/************************************************************/
+//sorts lowest to highest
+inline bool compareDistLinePairs(distlinePair left, distlinePair right){
+ return (left.end < right.end);
+}
//********************************************************************************************************************
//sorts lowest to highest
inline bool compareSequenceDistance(seqDist left, seqDist right){