Your code and samples are too complicated. Try to simplify it: show only the relevant data (for example, 2 or 3 columns in the files should be enough). Also, remove any logic that's not relevant to your question.

To be able to run your code, I first had to remove the filenames from the downloaded files, I then got a lot of warnings (why didn't you turn them on?) like: 

Odd number of elements in hash assignment at ./1.pl line 61.
Use of uninitialized value in list assignment at ./1.pl line 61.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value within %variants_geno in pattern match (m//
+) at ./1.pl line 100, <VAR> line 7.

[download]

The first two lines can be fixed by replacing the line with 

undef %variants_hash;

[download]

as the original was equivalent to 

%variants_hash = ( undef => );

[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

[download]

In reply to Re: error returning hash value? by choroba
in thread error returning hash value? by drlecb

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.