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/**
* logarithmic k-mer count based on a Bloom filter
* Copyright 2014 BCGSC
*/
#include "config.h"
#include "plc.h"
#include "CountingBloomFilter.h"
#include "Common/IOUtil.h"
#include "Common/Options.h"
#include "Common/StringUtil.h"
#include "DataLayer/Options.h"
#include <cassert>
#include <getopt.h>
#include <iostream>
#include <cstring>
#if _OPENMP
# include <omp.h>
#endif
using namespace std;
#define PROGRAM "logcounter"
static const char VERSION_MESSAGE[] =
PROGRAM " (" PACKAGE_NAME ") " VERSION "\n"
"Written by ?.\n"
"\n"
"Copyright 2014 Canada's Michael Smith Genome Science Centre\n";
static const char USAGE_MESSAGE[] =
"Usage: " PROGRAM " [OPTION]... [READS]...\n"
" -j, --threads=N use N parallel threads [1]\n"
" -k, --kmer=N the size of a k-mer\n"
" -s, --seed=N the seed value used\n"
" -b, --bloom-size=N size of bloom filter [500M]\n"
" --chastity discard unchaste reads [default]\n"
" --no-chastity do not discard unchaste reads\n"
" --trim-masked trim masked bases from the ends of reads\n"
" --no-trim-masked do not trim masked bases from the ends\n"
" of reads [default]\n"
" -q, --trim-quality=N trim bases from the ends of reads whose\n"
" quality is less than the threshold\n"
" --standard-quality zero quality is `!' (33)\n"
" default for FASTQ and SAM files\n"
" --illumina-quality zero quality is `@' (64)\n"
" default for qseq and export files\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
"\n"
"Report bugs to <" PACKAGE_BUGREPORT ">.\n";
namespace opt {
/** The number of parallel threads. */
static unsigned threads = 1;
/** The size of the bloom filter in bytes. */
size_t bloomSize = 500 * 1024 * 1024;
/** The size of a k-mer. */
unsigned k;
/** The seed value to use for random number gen **/
unsigned s;
// /** Prefix for output files */
// static string outputPrefix;
}
///** Counters */
//static struct {
//} g_count;
static const char shortopts[] = "j:k:s:q:v";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
{ "bloom-size", required_argument, NULL, 'b' },
{ "threads", required_argument, NULL, 'j' },
{ "kmer", required_argument, NULL, 'k' },
{ "seed", required_argument, NULL, 's' },
{ "chastity", no_argument, &opt::chastityFilter, 1 },
{ "no-chastity", no_argument, &opt::chastityFilter, 0 },
{ "trim-masked", no_argument, &opt::trimMasked, 1 },
{ "no-trim-masked", no_argument, &opt::trimMasked, 0 },
{ "trim-quality", required_argument, NULL, 'q' },
{ "standard-quality", no_argument, &opt::qualityOffset, 33 },
{ "illumina-quality", no_argument, &opt::qualityOffset, 64 },
{ "verbose", no_argument, NULL, 'v' },
{ "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;) {
istringstream arg(optarg != NULL ? optarg : "");
switch (c) {
case '?':
die = true; break;
case 'b':
opt::bloomSize = SIToBytes(arg); break;
case 'j':
arg >> opt::threads; break;
case 'k':
arg >> opt::k; break;
case 's':
arg >> opt::s; break;
case 'q':
arg >> opt::qualityThreshold; break;
case 'v':
opt::verbose++; break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
if (optarg != NULL && (!arg.eof() || arg.fail())) {
cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (opt::k == 0) {
cerr << PROGRAM ": missing mandatory option `-k'\n";
die = true;
}
if (die) {
cerr << "Try `" << PROGRAM
<< " --help' for more information.\n";
exit(EXIT_FAILURE);
}
#if _OPENMP
if (opt::threads > 0)
omp_set_num_threads(opt::threads);
#endif
//set seed
srand (opt::s);
Kmer::setLength(opt::k);
assert(opt::bloomSize > 0);
//size determined by
CountingBloomFilter<plc> bloom(opt::bloomSize, 1);
for (int i = optind; i < argc; i++)
Bloom::loadFile(bloom, opt::k, string(argv[i]), opt::verbose);
return 0;
}
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