assembly_algorithms.h

/*
 *  MEGAHIT
 *  Copyright (C) 2014 The University of Hong Kong
 *
 *  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/>.
 */

#ifndef ASSEMBLY_ALGORITHMS_H_
#define ASSEMBLY_ALGORITHMS_H_

#include <vector>
#include <string>
#include "succinct_dbg.h"

using std::vector;
using std::string;

namespace assembly_algorithms {

// traverse simple path
int64_t NextSimplePathNode(SuccinctDBG &dbg, int64_t curr_node); // return -1 if cannot extend
int64_t PrevSimplePathNode(SuccinctDBG &dbg, int64_t curr_node); // return -1 if cannot extend

// tips removal
int64_t Trim(SuccinctDBG &dbg, int len, int min_final_contig_len);
int64_t RemoveTips(SuccinctDBG &dbg, int max_tip_len, int min_final_contig_len);

// bubble merging
int64_t PopBubbles(SuccinctDBG &dbg, int max_bubble_len, double low_depth_ratio = 1);

// assembly

void AssembleFromUnitigGraph(SuccinctDBG &dbg, FILE *contigs_file, FILE *multi_file, FILE *final_contig_file, int min_final_contig_len);
void AssembleFinalFromUnitigGraph(SuccinctDBG &dbg, FILE *final_contig_file, int min_final_contig_len);
void RemoveLowLocalAndOutputChanged(SuccinctDBG &dbg, FILE *contigs_file, FILE *multi_file, FILE *final_contig_file, FILE *addi_contig_file, FILE *addi_multi_file, 
                                    double min_depth, int min_len, double local_ratio, int min_final_contig_len);
void RemoveLowLocalAndOutputFinal(SuccinctDBG &dbg, FILE *final_contig_file, 
                                  double min_depth, int min_len, double local_ratio, int min_final_contig_len);

// print stat
void PrintStat(long long genome_size = 0);

}

#endif // define ASSEMBLY_ALGORITHMS_H_