chromosome_utils.hpp

/*
 *    Part of SMITHLAB software
 *
 *    Copyright (C) 2014 University of Southern California and
 *                       Andrew D. Smith
 *
 *    Authors: Andrew D. Smith
 *
 *    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 CHROMOSOME_UTILS_HPP
#define CHROMOSOME_UTILS_HPP

#include <string>
#include <sstream>
#include <algorithm>
#include <vector>
#include <iostream>
#include <ostream>
#include <limits>
#include <iterator>
#include <cassert>
#include <cmath>

#include "GenomicRegion.hpp"

void
parse_region_name(std::string region_name,
                  std::string &chrom, size_t &start, size_t &end);


void
extract_regions_chrom_fasta(const std::string &chrom_name,
                            const std::string &filename,
                            const std::vector<GenomicRegion> &regions,
                            std::vector<std::string> &sequences);


void
extract_regions_chrom_fasta(const std::string &chrom_name,
                            const std::string &filename,
                            const std::vector<SimpleGenomicRegion> &regions,
                            std::vector<std::string> &sequences);


void
extract_regions_fasta(const std::string &dirname,
                      const std::vector<SimpleGenomicRegion> &regions_in,
                      std::vector<std::string> &sequences);


void
extract_regions_fasta(const std::string &dirname,
                      const std::vector<GenomicRegion> &regions_in,
                      std::vector<std::string> &sequences);


void
identify_chromosomes(const std::string chrom_file,
                     const std::string fasta_suffix,
                     std::unordered_map<std::string,
                                             std::string> &chrom_files);


void
identify_and_read_chromosomes(const std::string chrom_file,
                              const std::string fasta_suffix,
                              std::unordered_map<std::string,
                                                      std::string> &chrom_files);

#endif