(as long as it doesn't overflow the array element size)

With 16 meg combinations of 12 bps, and a 3 billion (-11 :) bps in all, it averages to 179 of each 12-char strings (assuming random data). I used a 4 bytes integer for each counter, so even if the sequence consisted of entirely one character, there is still plenty of headroom.

From some previous analysis I did on the Drosophila genome, the numbers of repeat sequences are quite low. In it's 160MB, repeats counts for subsequences of length 8 are in the low thousands and by the time you get to 12-chars rarely above a few hundred though you do get some 12-char combinations that run to several thousand repeats, particularly those involving T & A for some reason?

I coded a version of the above in XS that allows you to specify the element size as 2, 4 or 8 and it will detect attempts to assign values larger. I'm having trouble with conversion between __int64s and doubles for returning to Perl though.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

In reply to Re^3: A better (problem-specific) perl hash? by BrowserUk
in thread A better (problem-specific) perl hash? by srdst13

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.