Add an example

example.cpp

+#include "multicover.hpp"
+#include <iostream>
+#include <sdsl/rrr_vector.hpp>
+#include <sdsl/sd_vector.hpp>
+#include <string>
+
+template <class bv>
+void print_multicover_info(MultiCover<bv> &cover) {
+  std::cout << cover.getNbChromosomes() << " chromosomes in this .bam"
+            << std::endl << "Number of reads per chromosome" << std::endl;
+  for (size_t i = 0; i < cover.getNbChromosomes(); i++) {
+    std::cout << "\t" << cover.getChrName(i)
+              << "\t" << cover.getChrCoverage(i).count_reads_between(0, cover.getChrCoverage(i).nb_genome_positions()) << " reads" << std::endl;
+  }
+}
+
+int main(int argc, char **argv) {
+  if (argc <= 1) {
+    std::cerr << "Usage: " << argv[0] << " file.bam" << std::endl;
+    exit(1);
+  }
+  MultiCover<sd_vector<> > cover(argv[1]);
+
+  print_multicover_info(cover);
+  
+  // Generate a .bed.gz of the number of reads in every 1,000bp
+  // non-overlapping range
+  cover.generateBED(1000, std::string(argv[1])+".bed.gz");
+  
+  std::cout << "Saving the structure to disk" << std::endl;
+  cover.save(argv[1]);
+
+  std::cout << "Loading the structure that have just been saved" << std::endl;
+  MultiCover<sd_vector<> > cover2(argv[1], true);
+
+  cover2.generateBED(1000, std::string(argv[1])+"-2.bed.gz");
+  print_multicover_info(cover2);
+}