forked from homologus/Pandoras-Toolbox-for-Bioinformatics
/
main.cpp
35 lines (29 loc) · 1.08 KB
/
main.cpp
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//***************************************************************************
//* Copyright (c) 2011-2014 Saint-Petersburg Academic University
//* All Rights Reserved
//* See file LICENSE for details.
//****************************************************************************
#include <iostream>
#include "logging.hpp"
#include "options.hpp"
#include "quake.hpp"
namespace quake_enhanced {
DECL_LOGGER("main")
}
int main(int argc, char **argv) {
quake_enhanced::Options opts(argc, argv);
if (!opts.valid) {
std::cout << opts.help_message;
return 1;
}
quake_enhanced::Quake quake;
quake.Count(opts.read_file, opts.kmer_count_file,
opts.hash_file_prefix, opts.hash_file_number,
opts.quality_offset, opts.quality_threshold);
quake.PrepareHists(opts.hist_file, opts.trusted_hist_file,
opts.bad_hist_file, opts.top_threshold,
opts.average_min);
quake.PrepareLimits(opts.bad_threshold, opts.limits_file);
quake.FilterTrusted(opts.kmer_count_file, opts.trusted_hist_file, opts.bad_kmer_file);
return 0;
}