text: #!/usr/bin/env perl
  
  use strict;
  use FindBin;
  use lib ("$FindBin::RealBin/../../PerlLib");
  use SAM_reader;
  use SAM_entry;
  
  my $usage = "usage: $0 file.sam\n\n";
  
  my $sam_file = $ARGV[0] or die $usage;
  
  
  
  main: {
  
  	my $sam_reader = new SAM_reader($sam_file);
      
      
      my $filtered_count = 0;
      my $total_count = 0;
      
  
  	while ($sam_reader->has_next()) {
  		
  		my $sam_entry = $sam_reader->get_next();
          $total_count++;
          
          if (! $sam_entry->is_proper_pair()) {
              $filtered_count++;
          }
          else {
              print $sam_entry->toString() . "\n";
          }
      }
      
      print STDERR "-filtered $filtered_count of $total_count indiv read alignments as not proper pairs = " . sprintf("%.2f", $filtered_count / $total_count * 100) . "\% of alignments\n";
      
  	exit(0);
  
  }
  