kmc_query.cpp

/*
 * =====================================================================================
 *
 *       Filename:  kmer_query.cc
 *
 *    Description:  
 *
 *        Version:  1.0
 *        Created:  04/27/2016 08:48:26 AM
 *       Revision:  none
 *       Compiler:  gcc
 *
 *         Author:  Prashant Pandey (), ppandey@cs.stonybrook.edu
 *   Organization:  Stony Brook University
 *
 * =====================================================================================
 */
#include <iostream>
#include <algorithm>
#include <cstring>
#include <vector>
#include <set>
#include <bitset>
#include <cassert>
#include <fstream>

#include <time.h>
#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/resource.h>
#include <sys/stat.h>
#include <sys/time.h>
#include <sys/mman.h>

#include	"kmc_api/kmc_file.h"

using namespace std;

/* Print elapsed time using the start and end timeval */
void print_time_elapsed(string desc, struct timeval* start, struct timeval* end) 
{
	struct timeval elapsed;
	if (start->tv_usec > end->tv_usec) {
		end->tv_usec += 1000000;
		end->tv_sec--;
	}
	elapsed.tv_usec = end->tv_usec - start->tv_usec;
	elapsed.tv_sec = end->tv_sec - start->tv_sec;
	float time_elapsed = (elapsed.tv_sec * 1000000 + elapsed.tv_usec)/1000000.f;
	cout << desc << "Total Time Elapsed: " << to_string(time_elapsed) << " seconds" << endl;
}

//void getRandomKmers(int n, vector<CKmerAPI>& kmers)
//{
	//for (int j = 0; j < n; j++) {
		//char kmer[28] = {0};
		//for (int i = 0; i < 28; i++) {
			//kmer[i] = bases[rand()/4];
		//}
		//CKmerAPI kmc_kmer(28);
		//kmers.push_back(kmc_kmer.from_string(kmer));
	//}
//}

/* 
 * ===  FUNCTION  ======================================================================
 *         Name:  main
 *  Description:  
 * =====================================================================================
 */
int main ( int argc, char *argv[] )
{
	string filename = string(argv[1]);
	int num_query = atoi(argv[2]);
	int random = atoi(argv[3]);
	int dump = atoi(argv[4]);
	CKMCFile kmer_database_list;
	CKMCFile kmer_database_rand;
	vector<CKmerAPI> kmer_objects;
	CKmerAPI kmer(28);
	uint32_t counter;
	struct timeval start, end;
	struct timezone tzp;
	char bases[] = {'C', 'A', 'T', 'G'}; // A=1, C=0, T=2, G=3
	ofstream dumpfile;
	dumpfile.open("RandomKmer.dump");

	if (!kmer_database_list.OpenForListing(filename)) {
		cout << "Can not open the database file" << endl;
		return EXIT_FAILURE;
	}

	cout << "Reading kmers from the database list" << endl;
	if (random) {
		for (int j = 0; j < num_query; j++) {
			string kmer;
			for (int i = 0; i < 28; i++) {
				kmer += bases[rand()%4];
			}
			if (dump)
				dumpfile << kmer << endl;
			CKmerAPI kmc_kmer(28);
			kmer_objects.push_back(kmc_kmer.from_string(kmer));
		}
	} else {
	uint64_t i = 0;
	while (kmer_database_list.ReadNextKmer(kmer, counter)) {
		i++;
		kmer_objects.push_back(kmer);
	}
	cout << "Total kmers: " << i << endl;
	kmer_database_list.Close();
	}
	
	if (!kmer_database_rand.OpenForRA(filename)) {
		cout << "Can not open the database file" << endl;
		return EXIT_FAILURE;
	}
	srand(time(NULL));

	cout << "Querying kmers in the KMC database rand" << endl;
	gettimeofday(&start, &tzp);
	for (int i = 0; i < num_query; i++) {
		uint64_t id = rand()%kmer_objects.size();
		/*cout << "index: " << id << endl;*/
		if (!kmer_database_rand.CheckKmer(kmer_objects[id], counter)) {
			cout << "Can not find the kmer: " << kmer_objects[id].to_string() << endl;
			abort();
		}
	}
	gettimeofday(&end, &tzp);
	print_time_elapsed("", &start, &end);
	kmer_database_rand.Close();

	return EXIT_SUCCESS;
}				/* ----------  end of function main  ---------- */