use strict;
use warnings;

use Benchmark q{cmpthese};

my $str  = q{AGACGAGTA} x 12000;

my @toMask = (
   2 .. 6,
   78,
   506 .. 1473,
   4863,
   26290 .. 37907,
   107889 .. 107996);

my $resAndOrAndNot = andOrAndNot($str, \@toMask);
my $resAndRegex    = andRegex($str, \@toMask);
my $resSubstrList  = substrList($str, \@toMask);

die qq{Inconsistent\n}
   unless $resAndOrAndNot eq $resAndRegex
      and $resAndOrAndNot eq $resSubstrList;

my $rcAndOrAndNot = sub
   {
       my $ret = andOrAndNot($str, \@toMask);
       return;
   };

my $rcAndRegex = sub
   {
       my $ret = andRegex($str, \@toMask);
       return;
   };

my $rcSubstrList = sub
   {
       my $ret = substrList($str, \@toMask);
       return;
   };

cmpthese (-3,
   {
      andOrAndNot => $rcAndOrAndNot,
      andRegex    => $rcAndRegex,
      substrList  => $rcSubstrList,
   });

sub andOrAndNot
{
    my ($str, $raToMask) = @_;

    my $mask = qq{\xFF}     x length $str;
    my $x    = q{x}         x length $str;
    substr $mask, $_, 1, qq{\x00} for @$raToMask;

    my $masked = ($str & $mask) | ($x & ~ $mask);
    return $masked;
}

sub andRegex
{
    my ($str, $raToMask) = @_;

    my $mask = qq{\xFF}     x length $str;
    my $x    = q{x}         x length $str;
    substr $mask, $_, 1, qq{\x00} for @$raToMask;

    my $masked = $str & $mask;
    $masked =~ s{\x00}{x}g;
    return $masked;
}

sub substrList
{
    my ($str, $raToMask) = @_;
    substr $str, $_, 1, q{x} for @$raToMask;
    return $str;
}
[download]