/* This file is part of Jellyfish.
Jellyfish is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Jellyfish is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Jellyfish. If not, see .
*/
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
namespace err = jellyfish::err;
template
void compute_stats(reader_type& reader, uint64_t low, uint64_t high,
uint64_t& uniq, uint64_t& distinct, uint64_t& total,
uint64_t& max) {
uniq = distinct = total = max = 0;
while(reader.next()) {
if(reader.val() < low || reader.val() > high) continue;
uniq += reader.val() == 1;
total += reader.val();
max = std::max(max, reader.val());
++distinct;
}
}
int stats_main(int argc, char *argv[])
{
stats_main_cmdline args(argc, argv);
std::ifstream is(args.db_arg);
if(!is.good())
err::die(err::msg() << "Failed to open input file '" << args.db_arg << "'");
jellyfish::file_header header;
header.read(is);
jellyfish::mer_dna::k(header.key_len() / 2);
ofstream_default out(args.output_given ? args.output_arg : 0, std::cout);
if(!out.good())
err::die(err::msg() << "Error opening output file '" << args.output_arg << "'");
if(!args.upper_count_given)
args.upper_count_arg = std::numeric_limits::max();
uint64_t uniq = 0, distinct = 0, total = 0, max = 0;
if(!header.format().compare(binary_dumper::format)) {
binary_reader reader(is, &header);
compute_stats(reader, args.lower_count_arg, args.upper_count_arg, uniq, distinct, total, max);
} else if(!header.format().compare(text_dumper::format)) {
text_reader reader(is, &header);
compute_stats(reader, args.lower_count_arg, args.upper_count_arg, uniq, distinct, total, max);
} else {
err::die(err::msg() << "Unknown format '" << header.format() << "'");
}
out << "Unique: " << uniq << "\n"
<< "Distinct: " << distinct << "\n"
<< "Total: " << total << "\n"
<< "Max_count: " << max << "\n";
out.close();
return 0;
}