https://github.com/bcgsc/ntCard
Revision 741c9417282570a71c4042f0d2022493f26c4e49 authored by Johnathan Wong on 27 January 2020, 22:56:49 UTC, committed by GitHub on 27 January 2020, 22:56:49 UTC
* release 1.2.1 * ChangeLog: update version number Co-Authored-By: Lauren Coombe <lauren.e.coombe@gmail.com> Co-authored-by: Lauren Coombe <lauren.e.coombe@gmail.com>
1 parent b14e327
Tip revision: 741c9417282570a71c4042f0d2022493f26c4e49 authored by Johnathan Wong on 27 January 2020, 22:56:49 UTC
release 1.2.1 (#40)
release 1.2.1 (#40)
Tip revision: 741c941
nthll.cpp
#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <cstdlib>
#include <getopt.h>
#include <cassert>
#include <cmath>
#include "vendor/ntHash/ntHashIterator.hpp"
#include "Uncompress.h"
#ifdef _OPENMP
# include <omp.h>
#endif
#define PROGRAM "nthll"
static const char VERSION_MESSAGE[] =
PROGRAM " 1.2.1 \n"
"Written by Hamid Mohamadi.\n"
"Copyright 2018 Hamid Mohamadi, Licensed under MIT License\n";
static const char USAGE_MESSAGE[] =
"Usage: " PROGRAM " [OPTION]... FILE(S)...\n"
"Estimates distinct number of k-mers in FILE(S).\n\n"
"Acceptable file formats: fastq, fasta, sam, bam and in compressed formats gz, bz, zip, xz.\n"
"Accepts a list of files by adding @ at the beginning of the list name.\n"
"\n"
" Options:\n"
"\n"
" -t, --threads=N use N parallel threads [1] (N>=2 should be used when input files are >=2)\n"
" -k, --kmer=N the length of kmer [64]\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
"\n"
"Report bugs to https://github.com/bcgsc/ntCard/issues\n";
using namespace std;
namespace opt {
unsigned nThrd=1;
unsigned nHash=7;
unsigned kmLen=64;
unsigned nBuck=65536;
unsigned nBits=16;
unsigned sBuck=4194304;
unsigned sBits=22;
size_t totKmer=0;
bool canon=true;
bool samH=true;
}
static const char shortopts[] = "t:k:b:s:hc";
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' },
{ "sit", required_argument, NULL, 's' },
{ "hash", required_argument, NULL, 'h' },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
};
unsigned getftype(std::ifstream &in, std::string &samSeq) {
std::string hseq;
getline(in,hseq);
if(hseq[0]=='>') {
return 1;
}
if(hseq[0]=='@') {
if( (hseq[1]=='H'&& hseq[2]=='D') ||
(hseq[1]=='S'&& hseq[2]=='Q') ||
(hseq[1]=='R'&& hseq[2]=='G') ||
(hseq[1]=='P'&& hseq[2]=='G') ||
(hseq[1]=='C'&& hseq[2]=='O') ) {
return 2;
}
else
return 0;
}
opt::samH=false;
samSeq=hseq;
return 2;
}
inline void ntComp(const uint64_t hVal, uint8_t *mVec) {
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;
}
}
inline void ntRead(const string &seq, uint8_t *mVec) {
ntHashIterator itr(seq, 1, opt::kmLen);
while (itr != itr.end()) {
ntComp((*itr)[0], mVec);
++itr;
}
}
void getEfq(uint8_t *mVec, std::ifstream &in) {
bool good = true;
for(string seq, hseq; good;) {
good = static_cast<bool>(getline(in, seq));
good = static_cast<bool>(getline(in, hseq));
good = static_cast<bool>(getline(in, hseq));
if(good && seq.length()>=opt::kmLen)
ntRead(seq, mVec);
good = static_cast<bool>(getline(in, hseq));
}
}
void getEfa(uint8_t *mVec, std::ifstream &in) {
bool good = true;
for(string seq, hseq; good;) {
string line;
good = static_cast<bool>(getline(in, seq));
while(good&&seq[0]!='>') {
line+=seq;
good = static_cast<bool>(getline(in, seq));
}
if(line.length()>=opt::kmLen)
ntRead(line, mVec);
}
}
void getEsm(uint8_t *mVec, std::ifstream &in, const std::string &samSeq) {
std::string samLine,seq;
std::string s1,s2,s3,s4,s5,s6,s7,s8,s9,s11;
if(opt::samH) {
while(getline(in,samLine))
if (samLine[0]!='@') break;
}
else
samLine=samSeq;
do {
std::istringstream iss(samLine);
iss>>s1>>s2>>s3>>s4>>s5>>s6>>s7>>s8>>s9>>seq>>s11;
if(seq.length()>=opt::kmLen)
ntRead(seq, mVec);
} while(getline(in,samLine));
}
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 's':
arg >> opt::sBits;
break;
case 'k':
arg >> opt::kmLen;
break;
case 'c':
opt::canon=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]);
if(file[0]=='@') {
string inName;
ifstream inList(file.substr(1,file.length()).c_str());
while(getline(inList,inName))
inFiles.push_back(inName);
}
else
inFiles.push_back(file);
}
opt::nBuck = ((unsigned)1) << opt::nBits;
opt::sBuck = ((unsigned)1) << opt::sBits;
uint8_t *tVec = new uint8_t [opt::nBuck];
for (unsigned j=0; j<opt::nBuck; j++) tVec[j]=0;
#ifdef _OPENMP
omp_set_num_threads(opt::nThrd);
#endif
#pragma omp parallel
{
string fname;
uint8_t *mVec = new uint8_t [opt::nBuck];
for (unsigned j=0; j<opt::nBuck; j++) mVec[j]=0;
#pragma omp for schedule(dynamic) nowait
for (unsigned file_i = 0; file_i < inFiles.size(); ++file_i) {
fname = inFiles[inFiles.size()-file_i-1]; // verbose
std::ifstream in(inFiles[inFiles.size()-file_i-1].c_str());
std::string samSeq;
unsigned ftype = getftype(in,samSeq);
if(ftype==0)
getEfq(mVec, in);
else if (ftype==1)
getEfa(mVec, in);
else if (ftype==2)
getEsm(mVec, in, samSeq);
in.close();
}
#pragma omp critical(vmrg)
{
for (unsigned j=0; j<opt::nBuck; j++)
if(tVec[j]<mVec[j])
tVec[j]=mVec[j];
}
delete [] mVec;
}
double pEst = 0.0, zEst = 0.0, eEst = 0.0, alpha = 0.0;
alpha = 1.4426/(1 + 1.079/opt::nBuck);
if(opt::canon) alpha/=2;
for (unsigned j=0; j<opt::nBuck; j++)
pEst += 1.0/((uint64_t)1<<tVec[j]);
zEst = 1.0/pEst;
eEst = alpha * opt::nBuck * opt::nBuck * zEst;
delete [] tVec;
std::cout << "F0, Exp# of distnt kmers(k=" << opt::kmLen << "): " << (unsigned long long) eEst << "\n";
return 0;
}
Computing file changes ...