License: Apache 2.0
This is a set of C++ classes implementing various recursive n-gram hashing techniques, also called rolling hashing (http://en.wikipedia.org/wiki/Rolling_hash), including:
- Randomized Karp-Rabin (sometimes called Rabin-Karp)
- Hashing by Cyclic Polynomials (also known as Buzhash)
- Hashing by Irreducible Polynomials
This library is used by khmer: the in-memory nucleotide sequence k-mer engine.
const uint n(3);//hash all sequences of 3 characters
const uint L(7); // you need 7 bits
CyclicHash<uint32> hf(n,L );// if you want 64-bit values replace uint32 by uint64
for(uint32 k = 0; k<n;++k) {
chartype c = ... ; // grab some character
hf.eat(c); // feed it to the hasher
}
while(...) { // go over your string
hf.hashvalue; // at all times, this contains the hash value
chartype c = ... ;// point to the next character
chartype out = ...; // character we want to forget
hf.update(out,c); // update hash value
}
A recent GNU GCC C++ compiler or a recent CLANG.
type:
make
then
./unit
then
./speedtesting
- Daniel Lemire, Owen Kaser: Recursive n-gram hashing is pairwise independent, at best, Computer Speech & Language, Volume 24, Issue 4, October 2010, Pages 698-710 http://arxiv.org/abs/0705.4676
- Daniel Lemire, The universality of iterated hashing over variable-length strings, Discrete Applied Mathematics 160 (4-5), 2012. http://arxiv.org/abs/1008.1715
- Owen Kaser and Daniel Lemire, Strongly universal string hashing is fast, Computer Journal (2014) 57 (11): 1624-1638. http://arxiv.org/abs/1202.4961
This work has been used in genomics, see
- Ilia Minkin, Son Pham, Paul Medvedev, TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes, Bioinformatics (to appear). https://doi.org/10.1093/bioinformatics/btw609 and http://github.com/medvedevgroup/TwoPaCo