Not "flaws", but it's measuring performance per size of read buffer... (something LanX was saying needs tuning)

~$ perl vert4.pl
Benchmark: timing 3 iterations of 1, 10, 100, 1000, 10000, 100000, 100
+0000...
         1:  1 wallclock secs ( 0.94 usr +  0.01 sys =  0.95 CPU) @  3
+.16/s (n=3)
            (warning: too few iterations for a reliable count)
        10:  1 wallclock secs ( 0.23 usr +  0.02 sys =  0.25 CPU) @ 12
+.00/s (n=3)
            (warning: too few iterations for a reliable count)
       100:  0 wallclock secs ( 0.17 usr +  0.01 sys =  0.18 CPU) @ 16
+.67/s (n=3)
            (warning: too few iterations for a reliable count)
      1000:  0 wallclock secs ( 0.16 usr +  0.03 sys =  0.19 CPU) @ 15
+.79/s (n=3)
            (warning: too few iterations for a reliable count)
     10000:  0 wallclock secs ( 0.18 usr +  0.00 sys =  0.18 CPU) @ 16
+.67/s (n=3)
            (warning: too few iterations for a reliable count)
    100000:  0 wallclock secs ( 0.20 usr +  0.03 sys =  0.23 CPU) @ 13
+.04/s (n=3)
            (warning: too few iterations for a reliable count)
   1000000:  1 wallclock secs ( 0.23 usr +  0.03 sys =  0.26 CPU) @ 11
+.54/s (n=3)
            (warning: too few iterations for a reliable count)
[download]

use strict;
use warnings;

use Benchmark  qw{ cmpthese timethese };
use Test::More qw{ no_plan };

my $fn  = 'dna.txt';

unless ( -e $fn ) {
    open my $fh, '>', $fn;

    print $fh random_regex( '[ACTG]{42}' ), "\n"
        for 1 .. 1e6;
}

open my $inFH, q{<}, $fn or die $!;
my $offset = 9;    # Column 10 if numbering from 1

my @a = qw( 1 10 100 1000 10000 100000 1000000 );

sub method {
       seek $inFH, 0, 0;

       my $buffer     = <$inFH>;
       my $lineLen    = length $buffer;
#       my $nLines     = 500;
       my $nLines     = shift;
       my $chunkSize  = $lineLen * $nLines;

       seek $inFH, 0, 0;

       my $retStr;
       my $mask
          = qq{\x00} x ${offset}
          . qq{\xff}
          . qq{\x00} x ( $lineLen - $offset - 1 );
       $mask x= $nLines;
       while ( my $bytesRead = read $inFH, $buffer, $chunkSize )
       {
           ( my $anded = $buffer & $mask ) =~ tr{\x00}{}d;
           $retStr .= $anded;
       }

       return \ $retStr;
};


timethese( 3,
   {
       map { $_, "method( $_ )"} @a
   }
   );
[download]