+ string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".ref-query";
+ ofstream megAlignmentFile;
+ m->openOutputFile(megAlignmentFileName, megAlignmentFile);
+
+ for(int i=0;i<numRefs;i++){
+ megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
+ megAlignmentFile << megaAlignVector[i] << endl;
+ }
+
+