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Re: Sorting Gigabytes of Strings Without Storing Them

by grinder (Bishop)
on Dec 22, 2008 at 21:07 UTC ( #732187=note: print w/replies, xml ) Need Help??

in reply to Sorting Gigabytes of Strings Without Storing Them

One approach to save memory would be pack the strings using a custom mapping (A => 0x00, C => 0x01, G => 0x10, T => 0x11). This will allow you to store 4 characters in an 8-bit byte, thus consuming 9 bytes instead of 34. You probably want to do this anyway even if you sort with an external utility, since you'll improve bandwidth efficiencies the longer you can maintain the data in this compressed format.

Sadly your lengths are just two characters too many to hold everything in a nice 64-bit quantity.

• another intruder with the mooring in the heart of the Perl

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