The main issue really was that you provided an end position to substr while it expects a length. This has already been corrected by choroba above. I would like to propose to directly construct the intervals for the Ns under the assumption that your input intervals are sorted and non-overlapping. So instead of looking at 1 => 3, 5 => 6, etc I propose to add a zero at the beginning and the length of the string at the end to get 0 => 1, 3 => 5, 6 => ... which give you directly the intervals to put Ns into. 

use warnings;
use strict;

my $mask_input = '0000000000';
my %intervals = ( 0, ( do { local $/; <DATA> } =~ /(\d+)/g ), 1+length
+ $mask_input );

while( my( $start, $end ) = each %intervals ) {
        substr( $mask_input, $start, $end-$start-1 ) =~ tr/N/N/c;
}

print "$mask_input\n";

__DATA__
chrX      1      3
chrX      5      6
chrX      8      9

[download]

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

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.