/* 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
#include
namespace err = jellyfish::err;
template
void compute_histo(reader_type& reader, const uint64_t base, const uint64_t ceil,
uint64_t* histo, const uint64_t nb_buckets, const uint64_t inc) {
while(reader.next()) {
if(reader.val() < base)
++histo[0];
else if(reader.val() > ceil)
++histo[nb_buckets - 1];
else
++histo[(reader.val() - base) / inc];
}
}
int histo_main(int argc, char *argv[])
{
histo_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);
if(args.high_arg < args.low_arg)
histo_main_cmdline::error("High count value must be >= to low count value");
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 << "'");
const uint64_t base = args.increment_arg >= args.low_arg ? 0 : args.low_arg - args.increment_arg;
const uint64_t ceil = args.high_arg + args.increment_arg;
const uint64_t inc = args.increment_arg;
const uint64_t nb_buckets = (ceil + inc - base) / inc;
uint64_t* histo = new uint64_t[nb_buckets];
memset(histo, '\0', sizeof(uint64_t) * nb_buckets);
if(!header.format().compare(binary_dumper::format)) {
binary_reader reader(is, &header);
compute_histo(reader, base, ceil, histo, nb_buckets, inc);
} else if(!header.format().compare(text_dumper::format)) {
text_reader reader(is, &header);
compute_histo(reader, base, ceil, histo, nb_buckets, inc);
} else {
err::die(err::msg() << "Unknown format '" << header.format() << "'");
}
for(uint64_t i = 0, col = base; i < nb_buckets; ++i, col += inc)
if(histo[i] > 0 || args.full_flag)
out << col << " " << histo[i] << "\n";
delete [] histo;
out.close();
return 0;
}