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Commit 3f5b4fb0 authored by Veronique Legrand's avatar Veronique Legrand
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finished CMS component

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src/CountMinSketch.cpp
+ 56
− 29
View file @ 3f5b4fb0
......@@ -10,38 +10,65 @@
const int max_pow=30;
/* This method is used to determine if a number is a prime number or not.
* It is incomplete. TODO find an effective method to get lamdba prime numbers when we'll be sure whether we use the
* "prime number" version of the hash functions. */
/*int CountMinSketch::isPrime(unsigned int num) {
if ((num % 2 ==0) || (num==2)) return 0;
if ((num % 3 ==0) || (num==3)) return 0;
if ((num % 5 ==0) || (num==5)) return 0;
if ((num % 7 ==0) || (num==7)) return 0;
return 1;
}
int CountMinSketch::isMersenne(unsigned int num) {
int cur_pow=max_pow;
unsigned int mers_nbr=pow(2,cur_pow)-1;
while (num!=mers_nbr && cur_pow>=1) {
cur_pow-=1;
mers_nbr=pow(2,cur_pow)-1;
}
if (cur_pow==0) return 0;
else return 1;
// Store the non mersenne prime numbers for modulo hashing in this array.
int Pi_js[500]={
2147469629, 2147469637, 2147469659, 2147469679, 2147469703, 2147469781, 2147469817, 2147469823, 2147469829, 2147469881,\
2147469917, 2147469943, 2147469949, 2147469983, 2147470007, 2147470019, 2147470027, 2147470043, 2147470057, 2147470067,\
2147470081, 2147470111, 2147470123, 2147470139, 2147470147, 2147470177, 2147470183, 2147470211, 2147470229, 2147470249,\
2147470313, 2147470327, 2147470333, 2147470361, 2147470427, 2147470453, 2147470511, 2147470513, 2147470529, 2147470531,\
2147470553, 2147470579, 2147470597, 2147470603, 2147470627, 2147470643, 2147470673, 2147470679, 2147470723, 2147470727,\
2147470733, 2147470751, 2147470769, 2147470771,2147483059, 2147483069, 2147483077, 2147483123, 2147483137, 2147483171,\
2147473897, 2147473921, 2147473963, 2147474009, 2147474027, 2147474029, 2147474071, 2147474093, 2147474113, 2147474123,\
2147474149, 2147474159, 2147474201, 2147474213, 2147474239, 2147474279, 2147474359, 2147474383, 2147474393, 2147474477,\
2147474479, 2147474491, 2147474513, 2147474519, 2147474531, 2147474551, 2147474597, 2147474627, 2147474657, 2147474711,\
2147474717, 2147474789, 2147474803, 2147474807, 2147474809, 2147474831, 2147474837, 2147474843, 2147474851, 2147474881,\
2147474887, 2147474891, 2147474921, 2147474929, 2147474947, 2147474951, 2147474963, 2147475047, 2147475061, 2147475103,\
2147475107, 2147475149, 2147475179, 2147475181, 2147475193, 2147475203, 2147475221, 2147475229, 2147475233, 2147475251,\
2147475257, 2147475269, 2147475277, 2147475331, 2147475347, 2147475349, 2147475367, 2147475373, 2147475397, 2147475401,\
2147475413, 2147475439, 2147475481, 2147475487, 2147475497, 2147475503, 2147475509, 2147475521, 2147475541, 2147475553,\
2147475559, 2147475563, 2147475587, 2147475593, 2147475601, 2147475641, 2147475653, 2147475691, 2147475713, 2147475721,\
2147475739, 2147475787, 2147475791, 2147475797, 2147475829, 2147475851, 2147475859, 2147475871, 2147475899, 2147475929,\
2147475971, 2147475973, 2147475977, 2147475997, 2147476031, 2147476073, 2147476087, 2147476109, 2147476127, 2147476139,\
2147476141, 2147476169, 2147476183, 2147476211, 2147476249, 2147476291, 2147476321, 2147476327, 2147476367, 2147476381,\
2147476399, 2147476417, 2147476517, 2147476519, 2147476543, 2147476607, 2147476619, 2147476649, 2147476663, 2147476687,\
2147476693, 2147476699, 2147476739, 2147476741, 2147476763, 2147476769, 2147476777, 2147476789, 2147476819, 2147476823,\
2147476841, 2147476871, 2147476897, 2147476927, 2147476931, 2147476937, 2147476943, 2147476951, 2147476963, 2147476979,\
2147477021, 2147477029, 2147477063, 2147477093, 2147477107, 2147477113, 2147477159, 2147477191, 2147477201, 2147477203,\
2147477207, 2147477209, 2147477237, 2147477249, 2147477273, 2147477323, 2147477393, 2147477399, 2147477419, 2147477443,\
2147477467, 2147477473, 2147477503, 2147477513, 2147477531, 2147477533, 2147477599, 2147477627, 2147477681, 2147477687,\
2147477699, 2147477701, 2147477737, 2147477807, 2147477809, 2147477833, 2147477851, 2147477861, 2147477873, 2147477879,\
2147477881, 2147477933, 2147477953, 2147477989, 2147478013, 2147478017, 2147478049, 2147478079, 2147478083, 2147483179,\
2147478089, 2147478127, 2147478133, 2147478149, 2147478253, 2147478259, 2147478293, 2147478299, 2147478331, 2147478349,\
2147478373, 2147478461, 2147478481, 2147478491, 2147478497, 2147478503, 2147478517, 2147478521, 2147478563, 2147478569,\
2147478581, 2147478601, 2147478611, 2147478647, 2147478649, 2147478653, 2147478659, 2147478661, 2147478673, 2147478701,\
2147478703, 2147478719, 2147478721, 2147478727, 2147478731, 2147478733, 2147478763, 2147478791, 2147478821, 2147478859,\
2147478863, 2147478889, 2147478899, 2147478911, 2147478919, 2147478937, 2147478959, 2147478961, 2147478967, 2147478997,\
2147479013, 2147479031, 2147479057, 2147479063, 2147479079, 2147479091, 2147479097, 2147479121, 2147479129, 2147479133,\
2147479171, 2147479189, 2147479231, 2147479259, 2147479273, 2147479307, 2147479339, 2147479349, 2147479361, 2147479381,\
2147479403, 2147479421, 2147479447, 2147479489, 2147479507, 2147479513, 2147479517, 2147479531, 2147479547, 2147479549,\
2147479573, 2147479589, 2147479601, 2147479619, 2147479637, 2147479643, 2147479657, 2147479681, 2147479751, 2147479753,\
2147479757, 2147479781, 2147479787, 2147479819, 2147479823, 2147479879, 2147479891, 2147479897, 2147479907, 2147479937,\
2147479991, 2147480009, 2147480011, 2147480039, 2147480161, 2147480197, 2147480207, 2147480219, 2147480227, 2147480297,\
2147480299, 2147480311, 2147480327, 2147480369, 2147480429, 2147480437, 2147480459, 2147480471, 2147480507, 2147480519,\
2147480527, 2147480551, 2147480591, 2147480611, 2147480623, 2147480641, 2147480651, 2147480677, 2147480683, 2147480707,\
2147480723, 2147480743, 2147480747, 2147480791, 2147480837, 2147480843, 2147480849, 2147480893, 2147480897, 2147480899,\
2147480921, 2147480927, 2147480941, 2147480957, 2147480969, 2147480971, 2147480989, 2147481019, 2147481031, 2147481053,\
2147481071, 2147481139, 2147481143, 2147481151, 2147481173, 2147481179, 2147481199, 2147481209, 2147481247, 2147481263,\
2147481269, 2147481283, 2147481311, 2147481317, 2147481337, 2147481353, 2147481359, 2147481367, 2147481373, 2147481487,\
2147481491, 2147481499, 2147481509, 2147481529, 2147481563, 2147481571, 2147481629, 2147481673, 2147481793, 2147481797,\
2147481811, 2147481827, 2147481863, 2147481883, 2147481893, 2147481899, 2147481901, 2147481907, 2147481937, 2147481949,\
2147481967, 2147481997, 2147482021, 2147482063, 2147482081, 2147482091, 2147482093, 2147482121, 2147482223, 2147482231,\
2147482237, 2147482273, 2147482291, 2147482327, 2147482343, 2147482349, 2147482361, 2147482367, 2147482409, 2147482417,\
2147482481, 2147482501, 2147482507, 2147482577, 2147482583, 2147482591, 2147482621, 2147482661, 2147482663, 2147482681,\
2147482693, 2147482697, 2147482739, 2147482763, 2147482801, 2147482811, 2147482817, 2147482819, 2147482859, 2147482867,\
2147482873, 2147482877, 2147482921, 2147482937, 2147482943, 2147482949, 2147482951, 2147483029, 2147483033, 2147483053};
int CountMinSketch::hash64to32(unsigned long w,int j) {
int pi_j=Pi_js[j-1];
return w % pi_j;
}
void CountMinSketch::findNonMersPrime() {
int i;
unsigned int num=pi_j_max;
for (i=0;i<lambda;i++) {
num-=1;
while (!isPrime(num)) num-=1;
}
}*/
std::map<int,int> CountMinSketch::getIthArray(int i) {
std::map<int,int> tmp;
return tmp;
......
src/CountMinSketch.h
+ 28
− 17
View file @ 3f5b4fb0
......@@ -11,11 +11,16 @@
#include <vector>
#include <map>
typedef std::vector<unsigned long> readNumericValues; // TODO move this definition to a common include file between ReadProcessor and CountMinSketch.
#include "rock_commons.h"
typedef struct {
int lambda;
int kappa;
int kappa_prime;
} CMSparams;
class CountMinSketch {
static const unsigned int pi_j_max=2147483647;
static const unsigned long mask1=1;
static const unsigned long mask1=1; // used only for hash64to32bs
static const unsigned long mask2=2095103;
static const unsigned long mask3=1023;
......@@ -29,12 +34,12 @@ class CountMinSketch {
typedef std::map<int,short> internal_array;
std::vector<internal_array> cms_lambda_array;
std::vector<int> pi_j_array;
// std::vector<int> pi_j_array;
// void findNonMersPrime(); // fills pi_j_array with lambda non mersenne prime numbers.
// int hash64to32(unsigned long,int);
int hash64to32(unsigned long,int);
int hash64to32(unsigned long w,int j) { // bit shift version of hash function to start.
int hash64to32bs(unsigned long w,int j) { // bit shift version of hash function to start.
unsigned long h_tmp;
unsigned long h=~w;
h+=w<<18;
......@@ -57,14 +62,7 @@ class CountMinSketch {
void addKMer(unsigned long); // inline? TODO: see later if it can help us gain time.
int isRCovBelowThres(const readNumericValues& read_val,int threshold) ;
// for unit tests.
friend void test_CMS(int lambda,int kappa,int kappa_prime);
/*friend void test_findNonMersPrime(int lambda,int kappa,int kappa_prime);
friend void test_hash();*/
public:
CountMinSketch(int glambda,int gkappa,int gkappa_prime) {
void init(int glambda,int gkappa,int gkappa_prime) {
lambda=glambda;
kappa=gkappa;
kappa_prime=gkappa_prime;
......@@ -74,8 +72,21 @@ public:
for (j=0; j<lambda;j++) {
cms_lambda_array.push_back(cpt_array);
}
pi_j_array.reserve(lambda);
// findNonMersPrime();
}
// for unit tests.
friend void test_CMS(int lambda,int kappa,int kappa_prime);
/*
friend void test_hash();*/
public:
CountMinSketch(int glambda,int gkappa,int gkappa_prime) {
init(glambda,gkappa,gkappa_prime);
}
CountMinSketch(CMSparams parms) {
init(parms.lambda,parms.kappa,parms.kappa_prime);
}
......
src/unit_test_cms.cpp
+ 1
− 9
View file @ 3f5b4fb0
......@@ -26,15 +26,7 @@ void test_hash(int lambda,int kappa,int kappa_prime) {
}
}
void test_findNonMersPrime(int lambda,int kappa,int kappa_prime) {
CountMinSketch cms=CountMinSketch(lambda,kappa,kappa_prime);
assert(cms.pi_j_array.size()==lambda);
std::vector<int>::iterator it;
for (it=cms.pi_j_array.begin();it!=cms.pi_j_array.end();it++) {
assert(*it<CountMinSketch::pi_j_max);
}
assert(int (cms.pi_j_array[lambda-1])==2747483641);
}
*/
void test_CMS(int lambda,int kappa,int kappa_prime) {
CountMinSketch cms=CountMinSketch(lambda,kappa,kappa_prime);
......
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