Seems like an off by one error. I tried to fix it: 
#!/usr/bin/perl
use warnings;
use strict;

my $mask_input = '0000000000';

my $lastEnd = 0;
while (<DATA>) {
    my (undef, $start, $end) = split '\s+';
    my ($from, $length) = ($lastEnd, $start - $lastEnd);
    $length-- if $length > 0;

    substr($mask_input, $from, $length) =~ tr[\x00-\xff][N];
    $lastEnd = $end;
}
substr($mask_input, $lastEnd) =~ tr[\x00-\xff][N];

print "# Desired:  000N00N00N\n";
print "# Obtained: $mask_input\n";
print $mask_input eq '000N00N00N' ? "OK" : "Wrong", "\n";

__DATA__
chrX      1      3
chrX      5      6
chrX      8      9

[download]

Updated: fixed the initial value of $lastEnd. Thanks abualiga.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Trouble with Transliterate Function by choroba
in thread Trouble with Transliterate Function by ccelt09

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