+
+ if ( alignments.size() < 100 )
+ alignments.push_back(al);
+ }
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Unsorted Alignments" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::stable_sort(alignments.begin(), alignments.end(), Algorithms::Unsorted());
+ printAlignments(alignments);
+ cerr << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by name)" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Algorithms::SortByName<>());
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by tag Aq)" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Algorithms::SortByTag<int>("Aq"));
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+ cerr << endl
+ << "------------------------------" << endl
+ << "Sorted Alignments (by tag Aq) desc" << endl
+ << "------------------------------" << endl
+ << endl;
+ std::sort(alignments.begin(), alignments.end(), Algorithms::SortByTag<int, std::greater>("Aq"));
+ printAlignments(alignments);
+ cerr << endl
+ << "------------------------------" << endl
+ << endl;
+
+
+
+
+// // ########################################
+// // original
+// // ########################################
+//
+// while ( reader.GetNextAlignmentCore(al) )
+// ++alignmentCount;
+//
+// //#########################################