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/* 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 <http://www.gnu.org/licenses/>.
*/
#include <vector>
#include <jellyfish/err.hpp>
#include <jellyfish/thread_exec.hpp>
#include <jellyfish/file_header.hpp>
#include <jellyfish/stream_manager.hpp>
#include <jellyfish/whole_sequence_parser.hpp>
#include <jellyfish/mer_dna_bloom_counter.hpp>
#include <jellyfish/jellyfish.hpp>
#include "sequence_mers.hpp"
namespace err = jellyfish::err;
using jellyfish::mer_dna;
using jellyfish::mer_dna_bloom_counter;
typedef jellyfish::whole_sequence_parser<jellyfish::stream_manager<char**> > sequence_parser;
template<typename PathIterator, typename Database>
void query_from_sequence(PathIterator file_begin, PathIterator file_end, const Database& db,
bool canonical) {
jellyfish::stream_manager<PathIterator> streams(file_begin, file_end);
sequence_parser parser(4, 100, 1, streams);
sequence_mers mers(canonical);
const sequence_mers mers_end(canonical);
while(true) {
sequence_parser::job j(parser);
if(j.is_empty()) break;
for(size_t i = 0; i < j->nb_filled; ++i) {
std::cout << ">" << j->data[i].header << "\n";
mers = j->data[i].seq;
if(mers != mers_end) {
std::cout << db.check(*mers);
++mers;
}
for( ; mers != mers_end; ++mers)
std::cout << " " << db.check(*mers);
std::cout << "\n";
}
}
}
int main(int argc, char *argv[])
{
if(argc < 3)
err::die(err::msg() << "Usage: " << argv[0] << "db.jf file.fa [...]");
std::ifstream in(argv[1], std::ios::in|std::ios::binary);
jellyfish::file_header header(in);
if(!in.good())
err::die(err::msg() << "Failed to parse header of file '" << argv[1] << "'");
mer_dna::k(header.key_len() / 2);
if(header.format() == "bloomcounter") {
jellyfish::hash_pair<mer_dna> fns(header.matrix(1), header.matrix(2));
mer_dna_bloom_counter filter(header.size(), header.nb_hashes(), in, fns);
if(!in.good())
err::die("Bloom filter file is truncated");
in.close();
query_from_sequence(argv + 2, argv + argc, filter, header.canonical());
} else if(header.format() == binary_dumper::format) {
jellyfish::mapped_file binary_map(argv[1]);
binary_query bq(binary_map.base() + header.offset(), header.key_len(), header.counter_len(), header.matrix(),
header.size() - 1, binary_map.length() - header.offset());
query_from_sequence(argv + 2, argv + argc, bq, header.canonical());
} else {
err::die(err::msg() << "Unsupported format '" << header.format() << "'. Must be a bloom counter or binary list.");
}
return 0;
}
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