https://github.com/splatlab/squeakr
Revision 755ceefe33a9ef87482762f4381882c6ec974709 authored by Prashant Pandey on 30 November 2017, 16:57:50 UTC, committed by Prashant Pandey on 30 November 2017, 16:57:50 UTC
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Tip revision: 755ceefe33a9ef87482762f4381882c6ec974709 authored by Prashant Pandey on 30 November 2017, 16:57:50 UTC
Adding Squeakr exact.
Tip revision: 755ceef
hashutil.cc
/*
 * =====================================================================================
 *
 *       Filename:  hashutil.cc
 *
 *    Description:  
 *
 *        Version:  1.0
 *        Created:  04/18/2016 04:49:32 PM
 *       Revision:  none
 *       Compiler:  gcc
 *
 *         Author:  Prashant Pandey (ppandey@cs.stonybrook.edu)
 *                  Rob Patro (rob.patro@cs.stonybrook.edu)
 *                  Rob Johnson (rob@cs.stonybrook.edu)
 *   Organization:  Stony Brook University
 *
 * =====================================================================================
 */

#include "hashutil.h"


namespace kmercounting {

	//-----------------------------------------------------------------------------
	// MurmurHash2, 64-bit versions, by Austin Appleby

	// The same caveats as 32-bit MurmurHash2 apply here - beware of alignment 
	// and endian-ness issues if used across multiple platforms.


	// 64-bit hash for 64-bit platforms

	uint64_t HashUtil::MurmurHash64A ( const void * key, int len, unsigned int seed )
	{
		const uint64_t m = 0xc6a4a7935bd1e995;
		const int r = 47;

		uint64_t h = seed ^ (len * m);

		const uint64_t * data = (const uint64_t *)key;
		const uint64_t * end = data + (len/8);

		while(data != end)
		{
			uint64_t k = *data++;

			k *= m; 
			k ^= k >> r; 
			k *= m; 

			h ^= k;
			h *= m; 
		}

		const unsigned char * data2 = (const unsigned char*)data;

		switch(len & 7)
		{
			case 7: h ^= uint64_t(data2[6]) << 48;
			case 6: h ^= uint64_t(data2[5]) << 40;
			case 5: h ^= uint64_t(data2[4]) << 32;
			case 4: h ^= uint64_t(data2[3]) << 24;
			case 3: h ^= uint64_t(data2[2]) << 16;
			case 2: h ^= uint64_t(data2[1]) << 8;
			case 1: h ^= uint64_t(data2[0]);
							h *= m;
		};

		h ^= h >> r;
		h *= m;
		h ^= h >> r;

		return h;
	}


	// 64-bit hash for 32-bit platforms

	uint64_t HashUtil::MurmurHash64B ( const void * key, int len, unsigned int seed )
	{
		const unsigned int m = 0x5bd1e995;
		const int r = 24;

		unsigned int h1 = seed ^ len;
		unsigned int h2 = 0;

		const unsigned int * data = (const unsigned int *)key;

		while(len >= 8)
		{
			unsigned int k1 = *data++;
			k1 *= m; k1 ^= k1 >> r; k1 *= m;
			h1 *= m; h1 ^= k1;
			len -= 4;

			unsigned int k2 = *data++;
			k2 *= m; k2 ^= k2 >> r; k2 *= m;
			h2 *= m; h2 ^= k2;
			len -= 4;
		}

		if(len >= 4)
		{
			unsigned int k1 = *data++;
			k1 *= m; k1 ^= k1 >> r; k1 *= m;
			h1 *= m; h1 ^= k1;
			len -= 4;
		}

		switch(len)
		{
			case 3: h2 ^= ((unsigned char*)data)[2] << 16;
			case 2: h2 ^= ((unsigned char*)data)[1] << 8;
			case 1: h2 ^= ((unsigned char*)data)[0];
							h2 *= m;
		};

		h1 ^= h2 >> 18; h1 *= m;
		h2 ^= h1 >> 22; h2 *= m;
		h1 ^= h2 >> 17; h1 *= m;
		h2 ^= h1 >> 19; h2 *= m;

		uint64_t h = h1;

		h = (h << 32) | h2;

		return h;
	}

	/*
	 *   For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k),
	 *   which means
	 *     hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is
	 *     the inversion of
	 *       hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x,
	 *       mask), mask) == x.
	 */

	// Thomas Wang's integer hash functions. See
	// <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot.

	uint64_t HashUtil::hash_64(uint64_t key, uint64_t mask)
	{
		key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
		key = key ^ key >> 24;
		key = ((key + (key << 3)) + (key << 8)) & mask; // key * 265
		key = key ^ key >> 14;
		key = ((key + (key << 2)) + (key << 4)) & mask; // key * 21
		key = key ^ key >> 28;
		key = (key + (key << 31)) & mask;
		return key;
	}

	// The inversion of hash_64(). Modified from
	// <https://naml.us/blog/tag/invertible>
	uint64_t HashUtil::hash_64i(uint64_t key, uint64_t mask)
	{
		uint64_t tmp;

		// Invert key = key + (key << 31)
		tmp = (key - (key << 31));
		key = (key - (tmp << 31)) & mask;

		// Invert key = key ^ (key >> 28)
		tmp = key ^ key >> 28;
		key = key ^ tmp >> 28;

		// Invert key *= 21
		key = (key * 14933078535860113213ull) & mask;

		// Invert key = key ^ (key >> 14)
		tmp = key ^ key >> 14;
		tmp = key ^ tmp >> 14;
		tmp = key ^ tmp >> 14;
		key = key ^ tmp >> 14;

		// Invert key *= 265
		key = (key * 15244667743933553977ull) & mask;

		// Invert key = key ^ (key >> 24)
		tmp = key ^ key >> 24;
		key = key ^ tmp >> 24;

		// Invert key = (~key) + (key << 21)
		tmp = ~key;
		tmp = ~(key - (tmp << 21));
		tmp = ~(key - (tmp << 21));
		key = ~(key - (tmp << 21)) & mask;

		return key;
	}

}	// namespace kmercounting
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