https://github.com/bcgsc/ntCard
Revision 1f319301cb0662ced87dc7a6ab6c85b6149fdcf4 authored by mohamadi on 03 June 2016, 18:57:03 UTC, committed by mohamadi on 03 June 2016, 18:57:03 UTC
1 parent 2241563
Tip revision: 1f319301cb0662ced87dc7a6ab6c85b6149fdcf4 authored by mohamadi on 03 June 2016, 18:57:03 UTC
Initial parallel version
Initial parallel version
Tip revision: 1f31930
ntcards.cpp
#include <iostream>
#include <iomanip>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <cstdlib>
#include "nthash.hpp"
#include <getopt.h>
#define PROGRAM "ntcard"
static const char VERSION_MESSAGE[] =
PROGRAM " Version 1.0.0 \n"
"Written by Hamid Mohamadi.\n"
"Copyright 2016 Canada's Michael Smith Genome Science Centre\n";
static const char USAGE_MESSAGE[] =
"Usage: " PROGRAM " [OPTION]... QUERY\n"
"Report bugs to hmohamadi@bcgsc.ca.\n";
using namespace std;
namespace opt {
unsigned nThrd=1;
unsigned nHash=7;
unsigned kmLen=128;
unsigned nBuck=65536;
unsigned nBits=16;
bool fasta = false;
}
static const char shortopts[] = "k:b:h:t:f:c:";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
{ "threads", required_argument, NULL, 't' },
{ "kmer", required_argument, NULL, 'k' },
{ "bit", required_argument, NULL, 'b' },
{ "hash", required_argument, NULL, 'h' },
{ "fasta", no_argument, NULL, 'f' },
{ "canonical", no_argument, NULL, 'c' },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
};
int main(int argc, char** argv) {
bool die = false;
for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) {
std::istringstream arg(optarg != NULL ? optarg : "");
switch (c) {
case '?':
die = true;
break;
case 't':
arg >> opt::nThrd;
break;
case 'b':
arg >> opt::nBits;
break;
case 'h':
arg >> opt::nHash;
break;
case 'k':
arg >> opt::kmLen;
break;
case 'f':
opt::fasta=true;
break;
case OPT_HELP:
std::cerr << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
std::cerr << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
if (optarg != NULL && !arg.eof()) {
std::cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (argc - optind < 1) {
std::cerr << PROGRAM ": missing arguments\n";
die = true;
}
if (die) {
std::cerr << "Try `" << PROGRAM << " --help' for more information.\n";
exit(EXIT_FAILURE);
}
vector<string> inFiles;
for (int i = optind; i < argc; ++i) {
string file(argv[i]);
inFiles.push_back(file);
}
opt::nBuck = ((unsigned)1) << opt::nBits;
uint8_t *mVec = new uint8_t [opt::nBuck];
for (unsigned j=0; j<opt::nBuck; j++) mVec[j]=0;
for (unsigned file_i = 0; file_i < inFiles.size(); ++file_i) {
std::ifstream in(inFiles[file_i].c_str());
bool good = true;
for(string seq, hseq; good;) {
good = getline(in, hseq);
good = getline(in, seq);
good = getline(in, hseq);
good = getline(in, hseq);
if(good) {
string kmer = seq.substr(0, opt::kmLen);
uint64_t hVal = NTP64(kmer.c_str(), opt::kmLen);
if(hVal&(~((uint64_t)opt::nBuck-1))) {
uint8_t run0 = __builtin_clzll(hVal&(~((uint64_t)opt::nBuck-1)));
if(run0 > mVec[hVal&(opt::nBuck-1)]) mVec[hVal&(opt::nBuck-1)]=run0;
}
for (size_t i = 0; i < seq.length() - opt::kmLen; i++) {
hVal = NTP64(hVal, seq[i], seq[i+opt::kmLen], opt::kmLen);
if(hVal&(~((uint64_t)opt::nBuck-1))) {
uint8_t run0 = __builtin_clzll(hVal&(~((uint64_t)opt::nBuck-1)));
if(run0 > mVec[hVal&(opt::nBuck-1)]) mVec[hVal&(opt::nBuck-1)]=run0;
}
}
}
}
in.close();
}
double pEst = 0.0, zEst = 0.0, eEst = 0.0, alpha = 0.0;
alpha = 1.4426/(1 + 1.079/opt::nBuck);
for (unsigned j=0; j<opt::nBuck-1; j++)
pEst += 1.0/((uint64_t)1<<mVec[j]);
zEst = 1.0/pEst;
eEst = alpha * opt::nBuck * opt::nBuck * zEst;
std::cout << (unsigned long long) eEst << "\n";
delete [] mVec;
return 0;
}
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