local_assemble.cpp

/*
 *  MEGAHIT
 *  Copyright (C) 2014 - 2015 The University of Hong Kong & L3 Bioinformatics Limited
 *
 *  This program 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.
 *
 *  This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/* contact: Dinghua Li <dhli@cs.hku.hk> */

#include <string>
#include <omp.h>

#include "options_description.h"
#include "local_assembler.h"
#include "utils.h"

struct local_asm_opt_t {
    std::string contig_file;
    std::string lib_file_prefix;

    int kmin;
    int kmax;
    int step;
    int seed_kmer;

    int min_contig_len;
    int sparsity;
    double similarity;
    double min_mapping_len;

    int num_threads;
    std::string output_file;

    local_asm_opt_t() {
        kmin = 11;
        kmax = 41;
        step = 6;
        seed_kmer = 31;
        min_contig_len = 200;
        sparsity = 8;
        similarity = 0.95;
        min_mapping_len = 75;
        num_threads = 0;
        output_file = "";
    }
};

static local_asm_opt_t opt;

void ParseLocalAsmOptions(int argc, char *argv[]) {
    OptionsDescription desc;

    desc.AddOption("contig_file", "c", opt.contig_file, "contig file");
    desc.AddOption("lib_file_prefix", "l", opt.lib_file_prefix, "lib file prefix");
    desc.AddOption("kmin", "", opt.kmin, "");
    desc.AddOption("kmax", "", opt.kmax, "");
    desc.AddOption("step", "", opt.step, "");
    desc.AddOption("seed_kmer", "", opt.seed_kmer, "kmer size for seeding alignments");
    desc.AddOption("min_contig_len", "", opt.min_contig_len, "");
    desc.AddOption("min_mapping_len", "", opt.min_mapping_len, "");
    desc.AddOption("sparsity", "", opt.sparsity, "sparsity of hash mapper");
    desc.AddOption("similarity", "", opt.similarity, "alignment similarity threshold");
    desc.AddOption("num_threads", "t", opt.num_threads, "");
    desc.AddOption("output_file", "o", opt.output_file, "");

    try {
        desc.Parse(argc, argv);

        if (opt.contig_file == "") {
            throw std::logic_error("no contig file!");
        }

        if (opt.lib_file_prefix == "") {
            throw std::logic_error("no read file!");
        }

        if (opt.output_file == "") {
            throw std::logic_error("no output file!");
        }

        if (opt.num_threads == 0) {
            opt.num_threads = omp_get_max_threads();
        }
    }
    catch (std::exception &e) {
        std::cerr << e.what() << std::endl;
        std::cerr << "Usage: " << argv[0] << " -c contigs.fa -r reads.fq -o out.local_contig.fa" << std::endl;
        std::cerr << "options:" << std::endl;
        std::cerr << desc << std::endl;
        exit(1);
    }
}

int main_local(int argc, char **argv) {
    AutoMaxRssRecorder recorder;

    ParseLocalAsmOptions(argc, argv);

    omp_set_num_threads(opt.num_threads);

    LocalAssembler la(opt.min_contig_len, opt.seed_kmer, opt.sparsity);
    la.set_kmer(opt.kmin, opt.kmax, opt.step);
    la.set_mapping_threshold(opt.similarity, opt.min_mapping_len);
    la.set_num_threads(opt.num_threads);
    la.set_local_file(opt.output_file);

    la.ReadContigs(opt.contig_file);
    la.BuildHashMapper();
    la.AddReadLib(opt.lib_file_prefix);
    la.EstimateInsertSize();
    la.MapToContigs();
    la.LocalAssemble();

    return 0;
}