Here's just something that came to mind. Instead of using your massive if structure in ParseAChroms, you could try doing something a lot simpler, such as declaring what you're looking for in a sort of table: 
my %acrhom_prefix = (
    BAC         => '(.*)\s*',
    LENGTH      => '(.*)\s*',
    OSME        => '(.*)\s*',
    CHR_START   => '(.*)\s*',
    BAC_START   => '(.*)\s*',
    BAC_END     => '(.*)\s*',
    ORIENTATION => '(\w)\w*\s*',
);

[download]
Now, instead of using an "array" of variables, use a hash. This simplifies things massively: 
sub ParseAChroms
{
     my ($achromref) = @_;
     my (%value);
     foreach (@$achromref)
     {
          my ($prefix, $data) = /^(\S+):\s+(.*)/;
          if (my $pattern = $achrom_prefix{$prefix})
          {
               ($value{lc $prefix}) = $data =~ /^$pattern$/;
          }
     }

     return @data{qw[ type ac_id length
                      chr_num chr_start chr_end
                      bac_start bac_end orient]};
}

[download]
Now, I've just typed this into the editor here, so this is really just theory and not tested, but the idea is that this can be applied to a few other areas where you do the same thing.

Further, instead of passing arguments back and forth in a particular fixed order, why not return a HASH-ref? This makes it easy to add new data to the return value without breaking other functions which use it.

In reply to Re: Up for Critique by tadman
in thread Up for Critique by biograd

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.