(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.
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that isn't a hash, It's a (sparse) array.
Actually, it's a Perfect Hash.
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.
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[d/l] |