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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#include <boost/program_options.hpp>
#include "readsgetter.hpp"
#include "concurrenthash.hpp"
#include "graphdigger.hpp"
using namespace boost::program_options;
using namespace DeBruijn;
int main(int argc, const char* argv[]) {
for(int n = 0; n < argc; ++n)
cerr << argv[n] << " ";
cerr << endl << endl;
int kmer;
int ncores;
double vector_percent;
int min_count;
vector<string> sra_list;
vector<string> file_list;
size_t estimated_kmer_num;
options_description all("Options");
all.add_options()
("help,h", "Produce help message")
("version,v", "Print version")
#ifndef NO_NGS
("sra_run", value<vector<string>>(), "Input sra run accession (could be used multiple times for different runs) [string]")
#endif
("reads", value<vector<string>>(), "Input fasta/fastq file(s) (could be used multiple times for different runs) [string]")
("kmer", value<int>()->default_value(21), "Kmer length [integer]")
("min_count", value<int>()->default_value(2), "Minimal count for kmers retained for comparing alternate choices [integer]")
("vector_percent", value<double>()->default_value(0.05, "0.05"), "Count for vectors as a fraction of the read number (1. disables) [float (0,1]]")
("estimated_kmers", value<int>()->default_value(100), "Estimated number of unique kmers for bloom filter (millions) for hash count [integer]")
("skip_bloom_filter", "Don't do bloom filter; use --estimated_kmers as the hash table size for hash count [flag]")
("dbg_out", value<string>(), "De Bruijn graph output")
("text_out", value<string>(), "Text kmer output")
("hist", value<string>(), "File for histogram [string]")
("cores", value<int>()->default_value(0), "Number of cores to use (default all) [integer]");
try {
variables_map argm; // boost arguments
store(parse_command_line(argc, argv, all), argm);
notify(argm);
if(argm.count("help")) {
#ifdef SVN_REV
cout << "SVN revision:" << SVN_REV << endl << endl;
#endif
cout << all << "\n";
return 0;
}
if(argm.count("version")) {
cout << "kmercounter 2.1.0";
#ifdef SVN_REV
cout << "-SVN_" << SVN_REV;
#endif
cout << endl;
return 0;
}
if(!argm.count("reads")
#ifndef NO_NGS
&& !argm.count("sra_run")
#endif
) {
cerr << "Provide some input reads" << endl;
cerr << all << "\n";
return 1;
}
#ifndef NO_NGS
if(argm.count("sra_run")) {
sra_list = argm["sra_run"].as<vector<string>>();
unsigned num = sra_list.size();
sort(sra_list.begin(), sra_list.end());
sra_list.erase(unique(sra_list.begin(),sra_list.end()), sra_list.end());
if(sra_list.size() != num)
cerr << "WARNING: duplicate input entries were removed from SRA run list" << endl;
}
#endif
if(argm.count("reads")) {
file_list = argm["reads"].as<vector<string>>();
unsigned num = file_list.size();
sort(file_list.begin(), file_list.end());
file_list.erase(unique(file_list.begin(),file_list.end()), file_list.end());
if(file_list.size() != num)
cerr << "WARNING: duplicate input entries were removed from file list" << endl;
}
ncores = thread::hardware_concurrency();
if(argm["cores"].as<int>()) {
int nc = argm["cores"].as<int>();
if(nc < 0) {
cerr << "Value of --cores must be >= 0" << endl;
exit(1);
} else if(nc > ncores) {
cerr << "WARNING: number of cores was reduced to the hardware limit of " << ncores << " cores" << endl;
} else if(nc > 0) {
ncores = nc;
}
}
min_count = argm["min_count"].as<int>();
if(min_count <= 0) {
cerr << "Value of --min_count must be > 0" << endl;
exit(1);
}
estimated_kmer_num = argm["estimated_kmers"].as<int>();
kmer = argm["kmer"].as<int>();
CReadsGetter readsgetter(sra_list, file_list, vector<string>(), ncores, false);
vector_percent = argm["vector_percent"].as<double>();
if(vector_percent > 1.) {
cerr << "Value of --vector_percent must be <= 1" << endl;
exit(1);
}
if(vector_percent <= 0.) {
cerr << "Value of --vector_percent must be > 0" << endl;
exit(1);
}
if(vector_percent < 1.) {
readsgetter.ClipAdaptersFromReads_HashCounter(vector_percent, estimated_kmer_num, argm.count("skip_bloom_filter"));
readsgetter.PrintAdapters();
} else {
cerr << "Adapters clip is disabled" << endl;
}
size_t MB = 1000000;
CKmerHashCounter counter(readsgetter.Reads(), kmer, min_count, estimated_kmer_num*MB, true, ncores, argm.count("skip_bloom_filter"));
if(argm.count("text_out")) {
ofstream out(argm["text_out"].as<string>());
if(!out.is_open()) {
cerr << "Can't open file " << argm["text_out"].as<string>() << endl;
return 1;
}
CKmerHashCount& hash = counter.Kmers();
for(auto index = hash.Begin(); index != hash.End(); ++index) {
auto rslt = index.GetElement();
out << rslt.first.toString(kmer) << "\t" << rslt.second->Count() << "\t" << (rslt.second->m_data.Load() >> 32) << endl;
}
out.close();
if(!out) {
cerr << "Can't write to file " << argm["text_out"].as<string>() << endl;
return 1;
}
}
if(argm.count("hist")) {
ofstream out(argm["hist"].as<string>());
if(!out.is_open()) {
cerr << "Can't open file " << argm["hist"].as<string>() << endl;
return 1;
}
TBins bins = counter.Kmers().GetBins();
for(auto& bin : bins)
out << bin.first << '\t' << bin.second << endl;
out.close();
if(!out) {
cerr << "Can't write to file " << argm["hist"].as<string>() << endl;
return 1;
}
}
if(argm.count("dbg_out")) {
counter.GetBranches();
CDBHashGraph graph(move(counter.Kmers()), true);
ofstream dbg_out(argm["dbg_out"].as<string>(), ios::binary | ios::out);
if(!dbg_out.is_open()) {
cerr << "Can't open file " << argm["dbg_out"].as<string>() << endl;
exit(1);
}
graph.Save(dbg_out);
dbg_out.close();
if(!dbg_out) {
cerr << "Can't write to file " << argm["dbg_out"].as<string>() << endl;
return 1;
}
}
cerr << "DONE" << endl;
exit(0);
} catch (exception &e) {
cerr << endl << e.what() << endl;
exit(1);
}
}
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