+ struct linePair {
+ int start;
+ int numSeqs;
+ linePair(long int i, int j) : start(i), numSeqs(j) {}
+ };
+ vector<linePair*> lines;
+
+
+ string vertical, filter, fasta, hard, outputDir, filterFileName;
+ vector<string> fastafileNames;
+ int alignmentLength, processors;