The following code does what you want, ie. "Strand" can be at any position on the first line, and it removes the extreme memory overhead of reading in the whole file at once.

use warnings;
use strict;

use Data::Dumper;
use List::Util qw(first);

my %hits;
my $index;

open my $fh, '<', 'file.txt' or die $!;

while (<$fh>){
    chomp;
    my @F = split ' ';

    if (/Strand/){
        $index = first { $F[$_] eq 'Strand' } 0..$#F;
        next;
    }

    if (! exists $hits{$F[$index+1]}{$F[$index+2]}) {
        $hits{$F[$index+1]}{$F[$index+2]}{'w'} = 0;
        $hits{$F[$index+1]}{$F[$index+2]}{'c'} = 0;
    }
    $hits{$F[$index+1]}{$F[$index+2]}{$F[$index]}++;
}

print Dumper \%hits;

[download]

Data used:

Strand
1   4   1   0
1   5   1   0
1   31  1   0
1   74  1   0

[download]

In reply to Re^3: Memory usage while tallying instances of lines in a .txt file by stevieb
in thread Memory usage while tallying instances of lines in a .txt file by TJCooper

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