my $count = 0;
 44     my $priorScaffold;
 45     my $priorChr;
 46     my @finalArray;
 47     open (IN, '<', $fileName) or die "Cannot open $fileName\n";
 48     LINE: while (my $line = <IN>){
 49         chomp $line;
 50         if ($line =~ m/^>\w+/){
 51             next LINE;
 52         }
 53         my @dataLine = split /\t/, $line;
 54         my $chr = $dataLine[5];
 55         next LINE if ($chr !~ /^\d{1,2}?$/);
 56         my $scaffold = $dataLine[0];
 57         if ($count != 0){
 58             if ($scaffold ne $priorScaffold){                                       #If we found a new scaffoldd
 59                 push @{$global{$priorChr}{$priorScaffold}}, @finalArray;            #write to hash @finalArray using prior accumulated data for last scaffold    
 60                 $count = 0 ;
 61                 $allScaffolds{$priorScaffold}=0;                                    #Save priorScaffold in allScaffolds Hash for list use later- value is meaningless
 62                 @finalArray = ();
 63             }
 64             elsif ($chr != $priorChr){                                                 #If we just switched Chromosomes but are still on the same scaffold
 65                 push @{$global{$priorChr}{$priorScaffold}}, @finalArray;            #write to global the @finalArray accumulated to the point it switches chromosomes    
 66                 $count = 0;
 67                 @finalArray = ();
 68             }
 69         }
 70         push @{$finalArray[$count]},  @dataLine;
 71         $priorScaffold = $scaffold;
 72         $priorChr = $chr;
 73         $count ++;
 74         print "$line\n";
 75         print join ("\t", @dataLine)."\n";
 76     }